topo.coordmapper Package

---

coordmapper Package

A family of function objects for transforming one set of coordinates into another.

Coordinate mapper functions are useful for defining magnifications and other kinds of transformations on sheet coordinates, e.g. for defining retinal magnification using a CFProjection. A CoordinateMapperFn (e.g. MagnifyingMapper), is applied to an (x,y) pair and returns a new (x,y) pair. To apply a mapping to a CF projection, set the CFProjection’s coord_mapper parameter to an instance of the desired CoordinateMapperFn.

class topo.coordmapper.ReducingMapper(**params)

Bases: topo.coordmapper.SingleDimensionMapper

Provides a mapping that reduces the center of the activity.

Roughly the inverse of MagnifyingMapper. k indicates amount of reduction.

param Number in_range (allow_None=False, bounds=(0, None), constant=False, default=0.707106781187, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

The maximum range of the mapping input.

param Number k (allow_None=False, bounds=(0, None), constant=False, default=1.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

param Number out_range (allow_None=False, bounds=(0, None), constant=False, default=0.707106781187, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

The maximum range of the output.

param ObjectSelector remap_dimension (allow_None=None, check_on_set=True, compute_default_fn=None, constant=False, default=radius, instantiate=False, objects=[‘radius’, ‘x’, ‘y’, ‘xy’], pickle_default_value=True, precedence=None, readonly=False)

The dimension to remap. (‘xy’ remaps x and y independently.)

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa7da838>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa7da730>

inspect_value = <functools.partial object at 0x2b07aa7da2b8>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07aa7dad08>

set_param = <functools.partial object at 0x2b07aa7daa48>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.Scale2d(**kw)

Bases: topo.coordmapper.AffineTransform

Scale the input along the x and y axes by sx and sy, respectively.

param Number sy (allow_None=False, bounds=None, constant=False, default=1.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

param Number sx (allow_None=False, bounds=None, constant=False, default=1.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

param Parameter matrix (allow_None=False, constant=False, default=[[ 1. 1. 1.] [ 1. 1. 1.] [ 1. 1. 1.]], instantiate=False, pickle_default_value=True, precedence=None, readonly=False)

The affine transformation matrix. The functions Translate2dMat, Rotate2dMat, and Scale2dMat generate affine transform matrices that can be multiplied together to create combination transforms. E.g. the matrix:: Translate2dMat(3,0)*Rotate2d(pi/2) will shift points to the right by 3 units and rotate them around the origin by 90 degrees.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa7da3c0>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa7da838>

inspect_value = <functools.partial object at 0x2b07aa7da368>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07aa7daec0>

set_param = <functools.partial object at 0x2b07aa7da9f0>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.Jitter(**params)

Bases: topo.base.functionfamily.CoordinateMapperFn

Additively modifies calculated x,y coordinates, e.g. with random noise.

param Parameter scale (allow_None=False, constant=False, default=0.0, instantiate=False, pickle_default_value=True, precedence=None, readonly=False)

Amount of jitter.

param Parameter gen (allow_None=False, constant=False, default=<UniformRandom UniformRandom01315>, instantiate=False, pickle_default_value=True, precedence=None, readonly=False)

Number generator to use, typically a random distribution.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa7dad08>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa7da2b8>

inspect_value = <functools.partial object at 0x2b07aa7da3c0>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07aa7daba8>

set_param = <functools.partial object at 0x2b07aa7daf18>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.Cartesian2Polar(**params)

Bases: topo.base.functionfamily.CoordinateMapperFn

Maps from Cartesian (x,y) to polar (radius,angle).

param Boolean negative_radii (allow_None=False, bounds=(0, 1), constant=False, default=False, instantiate=False, pickle_default_value=True, precedence=None, readonly=False)

If true, coordinates with negative x values will be given negative radii, and angles between -90 and 90 degrees. (useful for mapping to saccade amplitude/direction space)

param Boolean degrees (allow_None=False, bounds=(0, 1), constant=False, default=True, instantiate=False, pickle_default_value=True, precedence=None, readonly=False)

Indicates whether the output angle is in degrees or radians.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa7da838>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa7da368>

inspect_value = <functools.partial object at 0x2b07aa7daec0>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07aa7da260>

set_param = <functools.partial object at 0x2b07aa7da940>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.OttesSCMotorMapper(**params)

Bases: topo.coordmapper.OttesSCMapper

Efferent superior colliculus mapping.

Provides the output/motor mapping from SC as defined by Ottes et al. (see superclass docs for reference)

The mapping allows the creation of a single sheet representing both colliculi, one in the x-positive hemisheet and the other in the x-negative hemisheet.

param Number A (allow_None=False, bounds=None, constant=False, default=5.3, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Shape parameter A, in degrees

param Number mm_scale (allow_None=False, bounds=None, constant=False, default=8.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Scale factor to convert constants Bu and Bv from mm to sheet units. Expressed in mm/unit.

param Number direction_scale (allow_None=False, bounds=None, constant=False, default=1, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Scale factor for saccade command direction, expressed in degrees per unit of sheet. Indicates what direction of saccade is represented by the y-component of the command input.

param Number Bu (allow_None=False, bounds=None, constant=False, default=1.8, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Rostral-caudal scale parameter, in mm

param Number Bv (allow_None=False, bounds=None, constant=False, default=1.8, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Orthogonal (medial-lateral?) scale paraemter in mm/deg

param Number amplitude_scale (allow_None=False, bounds=None, constant=False, default=1, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Scale factor for saccade command amplitude, expressed in degrees per unit of sheet. Indicates how large a saccade is represented by the x-component of the command input.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa7daba8>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa7daa48>

inspect_value = <functools.partial object at 0x2b07aa7daf18>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07aa7da3c0>

set_param = <functools.partial object at 0x2b07aa7da9f0>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.NormalJitter(**params)

Bases: topo.base.functionfamily.CoordinateMapperFn

Additively modifies calculated x,y coordinates with Gaussian random noise.

param Parameter gen (allow_None=False, constant=False, default=<NormalRandom NormalRandom01316>, instantiate=False, pickle_default_value=True, precedence=None, readonly=False)

Number generator to use, typically a Gaussian distribution.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa7da368>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa7daba8>

inspect_value = <functools.partial object at 0x2b07aa7da260>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07aa7da730>

set_param = <functools.partial object at 0x2b07aa7daec0>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.Pipeline(**params)

Bases: topo.base.functionfamily.CoordinateMapperFn

Applies a sequence of coordmappers, left to right.

param List mappers (allow_None=False, bounds=(0, None), constant=False, default=[], instantiate=True, pickle_default_value=True, precedence=None, readonly=False)

The sequence of mappers to apply.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa7da368>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa7daa48>

inspect_value = <functools.partial object at 0x2b07aa7da2b8>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07aa7daf18>

set_param = <functools.partial object at 0x2b07aa7da838>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.ConstantMapper(**params)

Bases: topo.base.functionfamily.CoordinateMapperFn

Map all values to the same constant, pre-specified coordinates.

param Number x_cons (allow_None=False, bounds=None, constant=False, default=0.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Constant x value returned by the mapping.

param Number y_cons (allow_None=False, bounds=None, constant=False, default=0.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Constant y value returned by the mapping.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa7daba8>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa7da260>

inspect_value = <functools.partial object at 0x2b07aa7da730>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07aa7da368>

set_param = <functools.partial object at 0x2b07aa7da940>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.MagnifyingMapper(**params)

Bases: topo.coordmapper.SingleDimensionMapper

Exponential (magnifying) mapping function.

Provides a mapping that magnifies the center of the activity image. Parameter k indicates amount of magnification, where 0 means no magnification.

param Number in_range (allow_None=False, bounds=(0, None), constant=False, default=0.707106781187, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

The maximum range of the mapping input.

param Number k (allow_None=False, bounds=(0, None), constant=False, default=1.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

param Number out_range (allow_None=False, bounds=(0, None), constant=False, default=0.707106781187, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

The maximum range of the output.

param ObjectSelector remap_dimension (allow_None=None, check_on_set=True, compute_default_fn=None, constant=False, default=radius, instantiate=False, objects=[‘radius’, ‘x’, ‘y’, ‘xy’], pickle_default_value=True, precedence=None, readonly=False)

The dimension to remap. (‘xy’ remaps x and y independently.)

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa7da730>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa7da2b8>

inspect_value = <functools.partial object at 0x2b07aa7daf18>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07aa7da9f0>

set_param = <functools.partial object at 0x2b07aa7daec0>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.AffineTransform(**kw)

Bases: topo.base.functionfamily.CoordinateMapperFn

Remaps the input with an affine transform.

This mapper allows the specification of an arbitrary combination of translation, rotation and scaling via a transform matrix. Single translations, etc, can be specified more simply with the subclasses Translate2d, Rotate2d, and Scale2d.

param Parameter matrix (allow_None=False, constant=False, default=[[ 1. 1. 1.] [ 1. 1. 1.] [ 1. 1. 1.]], instantiate=False, pickle_default_value=True, precedence=None, readonly=False)

The affine transformation matrix. The functions Translate2dMat, Rotate2dMat, and Scale2dMat generate affine transform matrices that can be multiplied together to create combination transforms. E.g. the matrix:: Translate2dMat(3,0)*Rotate2d(pi/2) will shift points to the right by 3 units and rotate them around the origin by 90 degrees.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa7da2b8>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa7da3c0>

inspect_value = <functools.partial object at 0x2b07aa7da368>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07aa7daba8>

set_param = <functools.partial object at 0x2b07aa7da838>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.SingleDimensionMapper(**params)

Bases: topo.base.functionfamily.CoordinateMapperFn

Coordinate Mapper that uses an origin-centered 1-D mapping function.

An abstract mapping function for coordinate mappers that remap based on the radius, x, or y individually. Subclasses should override _map_fn(self,z).

param Number in_range (allow_None=False, bounds=(0, None), constant=False, default=0.707106781187, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

The maximum range of the mapping input.

param Number out_range (allow_None=False, bounds=(0, None), constant=False, default=0.707106781187, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

The maximum range of the output.

param ObjectSelector remap_dimension (allow_None=None, check_on_set=True, compute_default_fn=None, constant=False, default=radius, instantiate=False, objects=[‘radius’, ‘x’, ‘y’, ‘xy’], pickle_default_value=True, precedence=None, readonly=False)

The dimension to remap. (‘xy’ remaps x and y independently.)

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa7daec0>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa86bd60>

inspect_value = <functools.partial object at 0x2b07aa86b050>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07963bb050>

set_param = <functools.partial object at 0x2b07963bb158>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.Polar2Cartesian(**params)

Bases: topo.base.functionfamily.CoordinateMapperFn

Map from polar (radius,angle) to Cartesian (x,y) coordinates.

param Boolean degrees (allow_None=False, bounds=(0, 1), constant=False, default=True, instantiate=False, pickle_default_value=True, precedence=None, readonly=False)

Indicates whether the input angle is in degrees or radians.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa86be10>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07aa86bd60>

inspect_value = <functools.partial object at 0x2b07963bb3c0>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07963bb998>

set_param = <functools.partial object at 0x2b07963bb050>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.Grid(**params)

Bases: topo.base.functionfamily.CoordinateMapperFn

Divides the 2D area into a grid, where all points within each grid element map to the same location.

param Number xdensity (allow_None=False, bounds=(0, None), constant=False, default=1, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Number of columns per 1.0 input sheet distance horizontally.

param Number ydensity (allow_None=False, bounds=(0, None), constant=False, default=1, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Number of rows per 1.0 input sheet distance vertically.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa86b100>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07963bb3c0>

inspect_value = <functools.partial object at 0x2b07963bb050>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07963bb998>

set_param = <functools.partial object at 0x2b07963bb578>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.Translate2d(**kw)

Bases: topo.coordmapper.AffineTransform

Translate the input by xoff,yoff.

param Number xoff (allow_None=False, bounds=None, constant=False, default=0.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

param Number yoff (allow_None=False, bounds=None, constant=False, default=0.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

param Parameter matrix (allow_None=False, constant=False, default=[[ 1. 1. 1.] [ 1. 1. 1.] [ 1. 1. 1.]], instantiate=False, pickle_default_value=True, precedence=None, readonly=False)

The affine transformation matrix. The functions Translate2dMat, Rotate2dMat, and Scale2dMat generate affine transform matrices that can be multiplied together to create combination transforms. E.g. the matrix:: Translate2dMat(3,0)*Rotate2d(pi/2) will shift points to the right by 3 units and rotate them around the origin by 90 degrees.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa86b6d8>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07963bb3c0>

inspect_value = <functools.partial object at 0x2b07963bb998>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07963bb050>

set_param = <functools.partial object at 0x2b07963bb890>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.OttesSCMapper(**params)

Bases: topo.base.functionfamily.CoordinateMapperFn

Abstract class for superior colliculus mappings.

Subclasses of this class implement afferent and efferent mappings from Ottes et al. (1986) Vision Research 26:857-873.

Default constant values are from Table 1, ibid.

param Number A (allow_None=False, bounds=None, constant=False, default=5.3, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Shape parameter A, in degrees

param Number mm_scale (allow_None=False, bounds=None, constant=False, default=8.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Scale factor to convert constants Bu and Bv from mm to sheet units. Expressed in mm/unit.

param Number direction_scale (allow_None=False, bounds=None, constant=False, default=1, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Scale factor for saccade command direction, expressed in degrees per unit of sheet. Indicates what direction of saccade is represented by the y-component of the command input.

param Number Bu (allow_None=False, bounds=None, constant=False, default=1.8, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Rostral-caudal scale parameter, in mm

param Number Bv (allow_None=False, bounds=None, constant=False, default=1.8, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Orthogonal (medial-lateral?) scale paraemter in mm/deg

param Number amplitude_scale (allow_None=False, bounds=None, constant=False, default=1, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Scale factor for saccade command amplitude, expressed in degrees per unit of sheet. Indicates how large a saccade is represented by the x-component of the command input.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa86be10>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07963bb890>

inspect_value = <functools.partial object at 0x2b07963bb998>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07963bb3c0>

set_param = <functools.partial object at 0x2b07963bb578>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.Rotate2d(**kw)

Bases: topo.coordmapper.AffineTransform

Rotate the input around the origin by an angle in radians.

param Number angle (allow_None=False, bounds=None, constant=False, default=0.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

param Parameter matrix (allow_None=False, constant=False, default=[[ 1. 1. 1.] [ 1. 1. 1.] [ 1. 1. 1.]], instantiate=False, pickle_default_value=True, precedence=None, readonly=False)

The affine transformation matrix. The functions Translate2dMat, Rotate2dMat, and Scale2dMat generate affine transform matrices that can be multiplied together to create combination transforms. E.g. the matrix:: Translate2dMat(3,0)*Rotate2d(pi/2) will shift points to the right by 3 units and rotate them around the origin by 90 degrees.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa86be10>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07963bb890>

inspect_value = <functools.partial object at 0x2b07963bb998>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07963bb3c0>

set_param = <functools.partial object at 0x2b07963bb158>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.OttesSCSenseMapper(**params)

Bases: topo.coordmapper.OttesSCMapper

Afferent superior colliculus mapping.

Provides the input/retinal mapping to SC as defined by Ottes et al. (see superclass docs for reference)

The mapping allows the creation of a single sheet representing both colliculi, one in the x-positive hemisheet and the other in the x-negative hemisheet.

[NOTE: see warning in docs for ottes_inverse_mapping().]

param Number A (allow_None=False, bounds=None, constant=False, default=5.3, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Shape parameter A, in degrees

param Number mm_scale (allow_None=False, bounds=None, constant=False, default=8.0, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Scale factor to convert constants Bu and Bv from mm to sheet units. Expressed in mm/unit.

param Number direction_scale (allow_None=False, bounds=None, constant=False, default=1, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Scale factor for saccade command direction, expressed in degrees per unit of sheet. Indicates what direction of saccade is represented by the y-component of the command input.

param Number Bu (allow_None=False, bounds=None, constant=False, default=1.8, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Rostral-caudal scale parameter, in mm

param Number Bv (allow_None=False, bounds=None, constant=False, default=1.8, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Orthogonal (medial-lateral?) scale paraemter in mm/deg

param Number amplitude_scale (allow_None=False, bounds=None, constant=False, default=1, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)

Scale factor for saccade command amplitude, expressed in degrees per unit of sheet. Indicates how large a saccade is represented by the x-component of the command input.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa86bec0>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07963bb998>

inspect_value = <functools.partial object at 0x2b07963bb158>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07963bb3c0>

set_param = <functools.partial object at 0x2b07963bbb50>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

class topo.coordmapper.CoordinateMapperFn(**params)

Bases: param.parameterized.Parameterized

Abstract base class for functions mapping from a 2D coordinate into another one.

debug(msg, *args, **kw)

Print msg merged with args as a debugging statement.

See Python’s logging module for details of message formatting.

defaults()

Return {parameter_name:parameter.default} for all non-constant Parameters.

Note that a Parameter for which instantiate==True has its default instantiated.

force_new_dynamic_value = <functools.partial object at 0x2b07aa86bec0>

get_param_values(onlychanged=False)

Return a list of name,value pairs for all Parameters of this object.

If onlychanged is True, will only return values that are not equal to the default value.

get_value_generator = <functools.partial object at 0x2b07963bb998>

inspect_value = <functools.partial object at 0x2b07963bb3c0>

message(msg, *args, **kw)

Print msg merged with args as a message.

See Python’s logging module for details of message formatting.

classmethod params(parameter_name=None)

Return the Parameters of this class as the dictionary {name: parameter_object}

Includes Parameters from this class and its superclasses.

pprint(imports=None, prefix=' ', unknown_value='<?>', qualify=False, separator='')

(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.

classmethod print_param_defaults()

Print the default values of all cls’s Parameters.

print_param_values()

Print the values of all this object’s Parameters.

script_repr(imports=, []prefix=' ')

Variant of __repr__ designed for generating a runnable script.

classmethod set_default(param_name, value)

Set the default value of param_name.

Equivalent to setting param_name on the class.

set_dynamic_time_fn = <functools.partial object at 0x2b07963bb158>

set_param = <functools.partial object at 0x2b07963bb890>

state_pop()

Restore the most recently saved state.

See state_push() for more details.

state_push()

Save this instance’s state.

For Parameterized instances, this includes the state of dynamically generated values.

Subclasses that maintain short-term state should additionally save and restore that state using state_push() and state_pop().

Generally, this method is used by operations that need to test something without permanently altering the objects’ state.

verbose(msg, *args, **kw)

Print msg merged with args as a verbose message.

See Python’s logging module for details of message formatting.

warning(msg, *args, **kw)

Print msg merged with args as a warning, unless module variable warnings_as_exceptions is True, then raise an Exception containing the arguments.

See Python’s logging module for details of message formatting.

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