Analysis tools for Topographica, other than plotting tools.
Configures the interface to the featuremapper and holoviews projects and sets the appropriate Topographica-specific hooks.
Topographica specific analysis commands, typically for measuring model activity or weights.
It implements several Topographica specific measurement commands, including weight matrix visualizations (e.g. update_projection).
Bases: param.parameterized.ParameterizedFunction
A callable Parameterized command for measuring or plotting a specified Sheet.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.SinusoidalMeasureResponseCommand
Measure an ocular dominance preference map by collating the response to patterns.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.PositionMeasurementCommand
Measure a corner preference map by collating the response to patterns.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: param.parameterized.ParameterizedFunction
Calculate center of gravity (CoG) for each CF of each unit in each CFSheet.
Unlike measure_position_pref and other measure commands, this one does not work by collating the responses to a set of input patterns. Instead, the CoG is calculated directly from each set of incoming weights. The CoG value thus is an indirect estimate of what patterns the neuron will prefer, but is not limited by the finite number of test patterns as the other measure commands are.
Measures only one projection for each sheet, as specified by the proj_name parameter. The default proj_name of ‘’ selects the first non-self connection, which is usually useful to examine for simple feedforward networks, but will not necessarily be useful in other cases.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Make a map of neural activity available for each sheet, for use in template-based plots.
This command simply asks each sheet for a copy of its activity matrix, and then makes it available for plotting. Of course, for some sheets providing this information may be non-trivial, e.g. if they need to average over recent spiking activity.
Bases: featuremapper.command.PositionMeasurementCommand
Generate the preference map for angle shapes, by collating the response to patterns.
param Integer positions (allow_None=False, bounds=None, constant=False, default=7, inclusive_bounds=(True, True), instantiate=False, pickle_default_value=True, precedence=None, readonly=False, time_dependent=True, time_fn=<Time Time00001>)
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.UnitCurveCommand
Measure spatial frequency preference of one unit of a sheet.
Uses an constant circular sine grating stimulus at the preferred with varying spatial frequency orientation and retinal position of the specified unit. Orientation and position preference must be calulated before measuring size response.
The curve can be plotted at various different values of the contrast (or actually any other parameter) of the stimulus. If using contrast and the network contains an LGN layer, then one would usually specify weber_contrast as the contrast_parameter. If there is no explicit LGN, then scale (offset=0.0) can be used to define the contrast. Other relevant contrast definitions (or other parameters) can also be used, provided they are defined in one of the appropriate metaparameter_fns.
param List contrasts (allow_None=False, bounds=(0, None), constant=False, default=[30, 60, 80, 90], instantiate=True, pickle_default_value=True, precedence=None, readonly=False)
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.FeatureCurveCommand
Measures orientation tuning curve(s) of a particular unit using a full-field sine grating stimulus.
The curve can be plotted at various different values of the contrast (or actually any other parameter) of the stimulus. If using contrast and the network contains an LGN layer, then one would usually specify michelson_contrast as the contrast_parameter. If there is no explicit LGN, then scale (offset=0.0) can be used to define the contrast. Other relevant contrast definitions (or other parameters) can also be used, provided they are defined in CoordinatedPatternGenerator and the units parameter is changed as appropriate.
param List contrasts (allow_None=False, bounds=(0, None), constant=False, default=[30, 60, 80, 90], instantiate=True, pickle_default_value=True, precedence=None, readonly=False)
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Return the centroid (center of gravity) for a 2D array.
Bases: featuremapper.command.UnitCurveCommand
Measures the response to a center sine grating disk and a surround sine grating ring at different contrasts of the central disk.
The central disk is set to the preferred orientation of the unit to be measured. The surround disk orientation (relative to the central grating) and contrast can be varied, as can the size of both disks.
param List contrasts (allow_None=False, bounds=(0, None), constant=False, default=[30, 60, 80, 90], instantiate=True, pickle_default_value=True, precedence=None, readonly=False)
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.SinusoidalMeasureResponseCommand
Measure a phase disparity preference map by collating the response to patterns.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.UnitCurveCommand
Measures contrast response curves for a particular unit.
Uses a circular sine grating stimulus at the preferred orientation and retinal position of the specified unit. Orientation and position preference must be calulated before measuring contrast response.
The curve can be plotted at various different values of the contrast (or actually any other parameter) of the stimulus. If using contrast and the network contains an LGN layer, then one would usually specify weber_contrast as the contrast_parameter. If there is no explicit LGN, then scale (offset=0.0) can be used to define the contrast. Other relevant contrast definitions (or other parameters) can also be used, provided they are defined in CoordinatedPatternGenerator and the units parameter is changed as appropriate.
param List relative_orientations (allow_None=False, bounds=(0, None), constant=False, default=[0.0, 0.5235987755982988, 0.7853981633974483, 1.5707963267948966], instantiate=True, pickle_default_value=True, precedence=None, readonly=False)
param List contrasts (allow_None=False, bounds=(0, None), constant=False, default=[10, 20, 30, 40, 50, 60, 70, 80, 90, 100], instantiate=True, pickle_default_value=True, precedence=None, readonly=False)
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.UnitCurveCommand
Measures orientation tuning curve(s) of a particular unit.
Uses a circular sine grating patch as the stimulus on the retina.
The curve can be plotted at various different values of the contrast (or actually any other parameter) of the stimulus. If using contrast and the network contains an LGN layer, then one would usually specify weber_contrast as the contrast_parameter. If there is no explicit LGN, then scale (offset=0.0) can be used to define the contrast. Other relevant contrast definitions (or other parameters) can also be used, provided they are defined in CoordinatedPatternGenerator and the units parameter is changed as appropriate.
param List contrasts (allow_None=False, bounds=(0, None), constant=False, default=[30, 60, 80, 90], instantiate=True, pickle_default_value=True, precedence=None, readonly=False)
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.SinusoidalMeasureResponseCommand
Measure an orientation preference map by collating the response to patterns.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.SinusoidalMeasureResponseCommand
Measure a direction preference map by collating the response to patterns.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Make available Red, Green, and Blue activity matrices for all appropriate sheets.
Bases: topo.analysis.command.UnitMeasurementCommand
A callable Parameterized command for measuring or plotting a unit from a Projection.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: topo.analysis.command.ProjectionSheetMeasurementCommand
Add SheetViews for all of the Projections of the ProjectionSheet specified by the sheet parameter, for use in template-based plots.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.SinusoidalMeasureResponseCommand
Measure preferences for sine gratings in various combinations. Can measure orientation, spatial frequency, spatial phase, ocular dominance, horizontal phase disparity, color hue, motion direction, and speed of motion.
In practice, this command is useful for any subset of the possible combinations, but if all combinations are included, the number of input patterns quickly grows quite large, much larger than the typical number of patterns required for an entire simulation. Thus typically this command will be used for the subset of dimensions that need to be evaluated together, while simpler special-purpose routines are provided below for other dimensions (such as hue and disparity).
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: topo.analysis.command.UnitMeasurementCommand
A callable Parameterized command for measuring or plotting units from a Projection.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: topo.analysis.command.ProjectionSheetMeasurementCommand
A callable Parameterized command for measuring or plotting specified units from a Sheet.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: param.parameterized.Parameterized
params(name=String)
Acts like a Python function, but with arguments that are Parameters.
Implemented as a subclass of Parameterized that, when instantiated, automatically invokes __call__ and returns the result, instead of returning an instance of the class.
To obtain an instance of this class, call instance().
[0m Object has no parameters.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.UnitCurveCommand
Measure receptive field size of one unit of a sheet.
Uses an expanding circular sine grating stimulus at the preferred orientation and retinal position of the specified unit. Orientation and position preference must be calulated before measuring size response.
The curve can be plotted at various different values of the contrast (or actually any other parameter) of the stimulus. If using contrast and the network contains an LGN layer, then one would usually specify weber_contrast as the contrast_parameter. If there is no explicit LGN, then scale (offset=0.0) can be used to define the contrast. Other relevant contrast definitions (or other parameters) can also be used, provided they are defined in CoordinatedPatternGenerator and the units parameter is changed as appropriate.
param List contrasts (allow_None=False, bounds=(0, None), constant=False, default=[30, 60, 80, 90], instantiate=True, pickle_default_value=True, precedence=None, readonly=False)
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.PositionMeasurementCommand
Measure a position preference map by collating the response to patterns.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: topo.analysis.featureresponses.pattern_present
This command is used to perform measurements, which require a number of permutations to complete. The inputs and outputs are defined as dictionaries corresponding to the generator sheets they are to be presented on and the measurement sheets to record from respectively. The update_activity_fn then accumulates the updated activity into the appropriate entry in the outputs dictionary.
The command also makes sure that time, events and state are reset after each presentation. If a GUI is found a timer will be opened to display a progress bar and sheet_views will be made available to the sheet to display activities.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.SinusoidalMeasureResponseCommand
Measure a hue preference map by collating the response to patterns.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.SingleInputResponseCommand
Map receptive fields by reverse correlation.
Presents a large collection of input patterns, typically white noise, keeping track of which units in the specified input_sheet were active when each unit in other Sheets in the simulation was active. This data can then be used to plot receptive fields for each unit. Note that the results are true receptive fields, not the connection fields usually presented in lieu of receptive fields, because they take all circuitry in between the input and the target unit into account.
Note also that it is crucial to set the scale parameter properly when using units with a hard activation threshold (as opposed to a smooth sigmoid), because the input pattern used here may not be a very effective way to drive the unit to activate. The value should be set high enough that the target units activate at least some of the time there is a pattern on the input.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.PatternPresentingCommand
Given a set of input patterns, installs them into the specified GeneratorSheets, runs the simulation for the specified length of time, then restores the original patterns and the original simulation time. Thus this input is not considered part of the regular simulation, and is usually for testing purposes.
May also be used to measure the response to a pattern by calling it with restore_events disabled and restore_state and install_sheetview enabled, which will push and pop the simulation state and install the response in the sheets views dictionary. The update_activity command implements this functionality.
As a special case, if ‘inputs’ is just a single pattern, and not a dictionary, it is presented to all GeneratorSheets.
If this process is interrupted by the user, the temporary patterns may still be installed on the retina.
If overwrite_previous is true, the given inputs overwrite those previously defined.
If plastic is False, overwrites the existing values of Sheet.plastic to disable plasticity, then re-enables plasticity.
If this process is interrupted by the user, the temporary patterns may still be installed on the retina.
In order to to see the sequence of values presented, you may use the back arrow history mechanism in the GUI. Note that the GUI’s Activity window must be open. Alternatively or access the activities through the Activity entry in the views.Maps dictionary on the specified sheets.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.SinusoidalMeasureResponseCommand
Measure the secondary orientation preference maps.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
FeatureResponses and associated functions and classes.
These classes implement map and tuning curve measurement based on measuring responses while varying features of an input pattern.
Bases: param.parameterized.Parameterized
Maintains a matrix of Distributions (each of which is a dictionary of (feature value: activity) pairs).
The matrix contains one Distribution for each unit in a rectangular matrix (given by the matrix_shape constructor argument). The contents of each Distribution can be updated for a given bin value all at once by providing a matrix of new values to update().
The results can then be accessed as a matrix of weighted averages (which can be used as a preference map) and/or a selectivity map (which measures the peakedness of each distribution).
Apply the given dsf DistributionStatisticFn on each element of the distribution_matrix
Return a dictionary of dictionaries, with the same structure of the called DistributionStatisticFn, but with matrices as values, instead of scalars
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Variant of __repr__ designed for generating a runnable script.
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Add a new matrix of histogram values for a given bin value.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: param.parameterized.Parameterized
Records the output of every unit in a sheet, for every combination of feature values. Useful for collecting data for later analysis while presenting many input patterns.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Variant of __repr__ designed for generating a runnable script.
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Add a new matrix of histogram values for a given bin value.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.PatternDrivenAnalysis
Systematically vary input pattern feature values and collate the responses.
A DistributionMatrix for each measurement source and feature is created. The DistributionMatrix stores the distribution of activity values for that feature. For instance, if the features to be tested are orientation and phase, we will create a DistributionMatrix for orientation and a DistributionMatrix for phase for each measurement source. The orientation and phase of the input are then systematically varied (when measure_responses is called), and the responses of all units from a measurement source to each pattern are collected into the DistributionMatrix.
The resulting data can then be used to plot feature maps and tuning curves, or for similar types of feature-based analyses.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.FeatureResponses
Calculate the receptive fields for all neurons using reverse correlation.
param Boolean continue_measurement (allow_None=False, bounds=(0, 1), constant=False, default=True, instantiate=False, pickle_default_value=True, precedence=None, readonly=False)
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.FeatureResponses
Measure and collect the responses to a set of features, for calculating feature maps.
For each feature and each measurement source, the results are stored as a preference matrix and selectivity matrix in the sheet’s sheet_views; these can then be plotted as preference or selectivity maps.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.FeatureResponses
Measures and collects the responses to a set of features, for calculating tuning and similar curves.
These curves represent the response of a measurement source to patterns that are controlled by a set of features. This class can collect data for multiple curves, each with the same x axis. The x axis represents the main feature value that is being varied, such as orientation. Other feature values can also be varied, such as contrast, which will result in multiple curves (one per unique combination of other feature values).
A particular set of patterns is constructed using a user-specified pattern_generator by adding the parameters determining the curve (curve_param_dict) to a static list of parameters (param_dict), and then varying the specified set of features. The input patterns will then be passed to the pattern_response_fn, which should return the measured responses for each of the requested sheets. Once the responses to all feature permutations has been accumulated, the measured curves are passed to the storage_fn and are finally returned.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: holoviews.core.dimension.Dimension
Specifies several parameters required for generating a map of one input feature.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
(Experimental) Pretty printed representation that may be evaluated with eval. See pprint() function for more details.
The pretty-printed label string for the Dimension
Applies the defined formatting to the value.
Pretty prints the dimension name and value using the format_string parameter, including the unit string (if set). Numeric types are printed to the stated rounding level.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Variant of __repr__ designed for generating a runnable script.
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.PatternPresentingCommand
Parameterized command for presenting input patterns and measuring responses.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.MeasureResponseCommand
Parameterized command for presenting sine gratings and measuring responses.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.MeasureResponseCommand
Parameterized command for measuring topographic position.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.MeasureResponseCommand
A callable Parameterized command for measuring the response to input on a specified Sheet.
Note that at present the input is actually presented to all input sheets; the specified Sheet is simply used to determine various parameters. In the future, it may be modified to draw the pattern on one input sheet only.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.SinusoidalMeasureResponseCommand
A callable Parameterized command for measuring tuning curves.
param List contrasts (allow_None=False, bounds=(0, None), constant=False, default=[30, 60, 80, 90], instantiate=True, pickle_default_value=True, precedence=None, readonly=False)
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.FeatureCurveCommand
Measures tuning curve(s) of particular unit(s).
param List contrasts (allow_None=False, bounds=(0, None), constant=False, default=[30, 60, 80, 90], instantiate=True, pickle_default_value=True, precedence=None, readonly=False)
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Return the feature preference for a particular unit.
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: featuremapper.command.PatternPresentingCommand
Given a set of input patterns, installs them into the specified GeneratorSheets, runs the simulation for the specified length of time, then restores the original patterns and the original simulation time. Thus this input is not considered part of the regular simulation, and is usually for testing purposes.
May also be used to measure the response to a pattern by calling it with restore_events disabled and restore_state and install_sheetview enabled, which will push and pop the simulation state and install the response in the sheets views dictionary. The update_activity command implements this functionality.
As a special case, if ‘inputs’ is just a single pattern, and not a dictionary, it is presented to all GeneratorSheets.
If this process is interrupted by the user, the temporary patterns may still be installed on the retina.
If overwrite_previous is true, the given inputs overwrite those previously defined.
If plastic is False, overwrites the existing values of Sheet.plastic to disable plasticity, then re-enables plasticity.
If this process is interrupted by the user, the temporary patterns may still be installed on the retina.
In order to to see the sequence of values presented, you may use the back arrow history mechanism in the GUI. Note that the GUI’s Activity window must be open. Alternatively or access the activities through the Activity entry in the views.Maps dictionary on the specified sheets.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: topo.analysis.featureresponses.pattern_present
This command is used to perform measurements, which require a number of permutations to complete. The inputs and outputs are defined as dictionaries corresponding to the generator sheets they are to be presented on and the measurement sheets to record from respectively. The update_activity_fn then accumulates the updated activity into the appropriate entry in the outputs dictionary.
The command also makes sure that time, events and state are reset after each presentation. If a GUI is found a timer will be opened to display a progress bar and sheet_views will be made available to the sheet to display activities.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Make a map of neural activity available for each sheet, for use in template-based plots.
This command simply asks each sheet for a copy of its activity matrix, and then makes it available for plotting. Of course, for some sheets providing this information may be non-trivial, e.g. if they need to average over recent spiking activity.
Bases: holoviews.core.operation.TreeOperation
Computes histogram of the difference in feature preference between pre- and post-synaptic neurons weighted by the connection strength between them.
param Boolean weighted (allow_None=False, bounds=(0, 1), constant=False, default=True, instantiate=False, pickle_default_value=True, precedence=None, readonly=False)
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
Returns the extents if all the elements of an overlay agree on a consistent extents, otherwise raises an exception.
Returns a label if all the elements of an overlay agree on a consistent label, otherwise returns the default label.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
The process_element method allows a single element to be operated on given an externally supplied key.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Helper method that returns a list of elements that match the given path pattern of form {type}.{group}.{label}.
The input may be a Layout, an Overlay type or a single Element.
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Bases: holoviews.core.operation.TreeOperation
Computes a histogram of azimuths between the positional preferences of pre- and post-synaptic neurons weighted by the connection strength and normalized relative to the orientation preference.
Useful for determining whether lateral connection are anisotropic along the axis of preferred orientation.
Print msg merged with args as a debugging statement.
See Python’s logging module for details of message formatting.
Return {parameter_name:parameter.default} for all non-constant Parameters.
Note that a Parameter for which instantiate==True has its default instantiated.
Returns the extents if all the elements of an overlay agree on a consistent extents, otherwise raises an exception.
Returns a label if all the elements of an overlay agree on a consistent label, otherwise returns the default label.
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.
Print msg merged with args as a message.
See Python’s logging module for details of message formatting.
Return the Parameters of this class as the dictionary {name: parameter_object}
Includes Parameters from this class and its superclasses.
Same as Parameterized.pprint, except that X.classname(Y is replaced with X.classname.instance(Y
Print the default values of all cls’s Parameters.
Print the values of all this object’s Parameters.
The process_element method allows a single element to be operated on given an externally supplied key.
Same as Parameterized.script_repr, except that X.classname(Y is replaced with X.classname.instance(Y
Helper method that returns a list of elements that match the given path pattern of form {type}.{group}.{label}.
The input may be a Layout, an Overlay type or a single Element.
Set the default value of param_name.
Equivalent to setting param_name on the class.
Restore the most recently saved state.
See state_push() for more details.
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.
Print msg merged with args as a verbose message.
See Python’s logging module for details of message formatting.
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.
Returns the distance between a and b (scalars) in a domain with period period.