optimizer Package

Core Module

cmd_line Module

fitnessFunctions Module

graphic Module

modelHandler Module

class optimizer.modelHandler.externalHandler(command)

Handles models which are using a simulator other than Neuron. :param command: the command string which should be executed

Note

The command must consist of the following parts:

• the command to execute
• the model file
• options (optional)
• number of parameters to optimize

CreateStimuli(s)

GetExec()

Creates the command that runs the simulator with the model and with the appropriate options. :return: a list of strings ready for execution

GetParameters()

SetNParams(o)

Sets the number of parameters in the given object by calling it’s SetObjTOOpt method.

Parameters:o – the object whose method will be called

Note

This is necessary because the other parts expects that the option handler objects knows the parameters subjects to optimization. Since this is not true in the case of an external simulator, this workaround is needed.

SetStimuli(p, e)

class optimizer.modelHandler.modelHandlerNeuron(model_path, special_path, base='/home/docs/checkouts/readthedocs.org/user_builds/optimizer/checkouts/latest/doc')

Imports the necessary modules to handle Neuron models and loads the model as well as the additional mechanisms. Creates containers for the sections and the channels for easier handling.

Parameters:

• model_path – the path to the model file
• special_path – the path to the special file (.mod files)
• base – the base working directory

CreateStimuli(stims)

Creates a Neuron pointprocess which is responsible for the stimulation of the model.

Note

The type of the point process is either an IClamp or a SEClamp.

Parameters:stims –

a list with the following values:

• stimulation type as string
• position inside section
• name of the section

GetParameters()

Collects every member of every section object and filters out those that are not parameters of the model. The function will collect:

• every parameter of the the mechanisms
• every mechanism
• some default parameters that are always included in a model, and pointprocesses that are not some sort of Clamp

Returns:the filtered content of the model in a string matrix

Recordings(vector)

Converts the hoc vector obtained from the simulation and converts it into a Trace object.

Parameters:vector – a hoc vector Returns:the data trace from the created object

RunControll(settings)

Sets up the recording procedure and the simulation, then runs it.

Parameters:settings –

the settings of the recording and the parameters of the simulation:

• length of simulation
• integration step size
• parameter to record
• section to record from
• position inside the section
• initial voltage

SetChannelParameters(section, segment, channel, params, values)

Sets the given channel’s parameter to the given value. If the section is not known that indicates a serious internal error and the program will abort.

Parameters:

• section – the selected section’s name as string
• channel – the selected channel’s name as string
• params – the selected channel parameter’s name as string
• values – the value to be set

SetCustStimuli(params)

Uses the vector.play method from Neuron to create a time varying stimulus. The stimulus is read from the given file.

Parameters:params – list with the name of the file containing the stimulus as first element

Note

The delay value must be set to zero and the duration must be set to 1e9, but these are not the actual parameters of the stimulus. This is necessary for Neuron in order to work.

SetMorphParameters(section, params, values)

Sets the given morphological parameter to the given value. If the section is not known that indicates a serious internal error and the program will abort. If the section has no parameter with the given name then it is interpreted as a parameter of a pointprocess and the function will set the parameter assuming the pointprocess exists in the middle (0.5) at the given section and there is only one other pointprocess in the section.

Note

This workaround is implemented because some mechanisms are implemented as pointprocesses.

param section:the name of the section as string param params:the name of the parameter as string param values:the value to set

SetStimuli(params, extra_params)

Sets the parameters of the stimulating object. The parameters are the following:

• amplitude
• delay
• duration

or

• amplitude1
• amplitude2
• amplitude3
• duration1
• duration2
• duration3

Parameters:

• params – the list of parameters containing the first 3 values from the above list
• extra_params – list of parameters containing additional values to set up the SEClamp

Note

The rs parameter of the SEClamp is set to 0.01

contains(string, ss)

Checks if substring is in the given list and creates a string which contains only the matching elements separated by spaces.

Parameters:

• string – list of strings
• ss – the substring to be matched

Returns:

a string which contains only the matching elements separated by spaces

optimizer Module

optimizer.optimizer.main(parameters)

The main function, which starts to software according to the given command line arguments.

Parameters:parameters – the command line parameters: * -h help * -c command line * -g graphic interface

optimizerHandler Module

optionHandler Module

class optimizer.optionHandler.optionHandler

Bases: object

Object to store the settings required by the optimization work flow.

GetFileOption()

Returns:the current working directory (referred as base in modelHandler, used in traceReader )

GetFitnessParam()

Gets the parameters required by the fitness functions:

• list consisting of:

  • a dictionary containing the spike detection threshold and the spike window
  • a list of fitness function names

• list of weights to combine the fitness functions

Returns:a list containing the structures described above

GetInputOptions()

Gets the input related settings:

• input file
• number of traces in file
• unit of input
• length of the individual traces (see traceHandler)
• sampling frequency of the trace(s)
• flag indicating if file included time scale or not (will be removed, see traceHandler)
• the type of the trace(s)

Returns:the parameters listed above in a list

GetModelOptions()

Gets the model related options:

• path to the model
• path to the directory containing the special files (see modelHanlder)

Returns:the parameters listed above in a list

GetModelRun()

Gets the parameters corresponding to the simulation:

• length of simulation
• integration step
• parameter to record
• section name
• position inside the section
• initial voltage

Returns:the parameters above in a list

GetModelStim()

Gets the parameters regarding the stimulus type:

• type of the stimulus
• position of stimulus
• name of the stimulated section

Returns:the parameters listed above in a list

GetModelStimParam()

Gets the parameters of the stimulus:

• amplitude
• delay
• duration

Returns:the parameters listed above in a list

GetObjTOOpt()

Gets the parameters selected to optimization.

Returns:a list of strings

GetOptParam()

Not in use! Gets the list of parameter values corresponding to the parameters subject to optimization.

Returns:list of real values

GetOptimizerOptions()

Gets the parameters regarding the optimization process:

• seed: random seed
• evo_strat: name of evolution algorithm
• Size of Population: size of population
• Number of Generations: number of generations
• Mutation Rate: mutation rate (0-1)
• Cooling Rate: cooling rate (0-1)
• Mean of Gaussian: mean value of gaussian
• Std. Deviation of Gaussian: standard deviation of gaussian
• Cooling Schedule: index of cooling schedule
• Initial Temperature: initial temperature
• Final Temperature: final temperature
• Accuracy: accuracy
• Dwell: number of evaluation on the given temperature level
• Error Tolerance for x: error tolerance for input values
• Error Tolerance for f: error tolerance for fitness values
• num_params: number of input parameters
• boundaries: bounds of the parameters
• starting_points: initial values to the algorithm

Returns:a dictionary containing the parameters above

GetSimParam()

Gets the simulator related parameters:

• the name of the simulator
• the command which should be executed to run the model (see modelHandler)

Returns:the parameters listed above in a list

GetUFunString()

Gets the user defined function.

Returns:the function as a string

SetFileOptions(options)

Sets the current working directory

Parameters:options – the path of the directory

SetFitnesParam(options)

Sets the parameters required by the fitness functions.

Parameters:options – the required values in the structure described in GetFitnessParam

SetInputOptions(options)

Sets the options related to the input to the given values.

Parameters:options – a list of values (order of parameter should be the same as listed in GetInputOptions)

SetModelOptions(options)

Sets the model related options.

Parameters:options – a list of values

SetModelRun(options)

Sets the parameters regarding the simulation to the given values.

Parameters:options – list of parameters

SetModelStim(options)

Sets the parameters regarding the stimulus type to the given values.

Parameters:options – list of values

SetModelStimParam(options)

Sets the parameters of the stimulus to the given values.

Parameters:options – list of values

Note

Only the parameters of the IClamp are stored this way since the parameters of the SEClamp are obtained by combining the values here and the values regarding the simulation.

SetObjTOOpt(options)

Adds the given parameter to the list of parameters selected for optimization.

Parameters:options – a string containing the section, a channel name and a channel parameter name, or a morphological parameter separated by spaces

Note

If a given parameter is already stored then it will not added to the list.

SetOptParam(options)

Not in use! Adds the given value to the list of parameter values corresponding to the parameters subject to optimization.

Parameters:options – a real value

SetOptimizerOptions(options)

Sets the parameters regarding the optimization process.

Parameters:options – a dictionary containing the parameters

SetSimParam(options)

Sets the simulator related parameters.

Parameters:options – a list of values

SetUFunString(s)

Sets the user defined function.

Parameters:s – the function as a string

dump(f_mapper)

Dumps the content of the class into a string.

Parameters:f_mapper – a dictionary that maps the fitness function objects to their names (used in the GUI) Returns:the content of the class as string

read_all(root)

Reads settings from an xml tree and converts them to the necessary type.

Parameters:root – the root of the xml tree

Note

If there is an element in the tree whose tag is not a valid option name, then AttributeError is raised.

Note

The program does not verify if every parameter which are needed to the current process is present. We strongly recommend that you use the GUI to create a configuration file, which will contain the needed values, instead of writing the xml file by hand.

optimizer.optionHandler.prettify(e)

Converts the given xml tree object to human readable form.

Parameters:e – the xml tree element Returns:the reformatted content of the xml tree as string

traceHandler Module

class optimizer.traceHandler.DATA

The main data container class. :attr: data: holds the Trace object which contains the trace set

Note

This class will be able to hold multiple data sets with multiple types.

PyNNReader(path, no_traces, scale, t_length, freq, trace_type)

Reads a default recording result from PyNN with 9 line of headers (the parameters are the same as in the Read function)

Returns:a trace object holding the content of the file

Note

If the given file is not accessible the program will abort.

Note

If the number of traces in the file and the corresponding parameter is not equal, a sizeError is raised.

Read(path=['/home/docs/checkouts/readthedocs.org/user_builds/optimizer/checkouts/latest/doc/inputTrace.txt'], no_traces=1, scale='mV', t_length=1000, freq=1000, trace_type='voltage')

The main reader function. This calls the recognition function detect_format and uses the obtained reader function to read the data.

Parameters:path – list of data path(s) (currently only one file is handled)

(see the explanation of the other parameters in the description of Trace)

Note

The function uses the 5. line of the file for recognition.

abstractDataReader(path)

convert(dict_to_conv)

detect_format(line)

Automatically detects the format of the file and returns a reader functions which can process it correctly. The recognized formats are the following:

• simple text file with data columns separated by “\t”
• simple text file, containing time trace as well and data columns separated by “\t”
• default recording result from PyNN with 9 line of headers
• spike timing file from PyNN with 9 line of headers (not used)

Parameters:line – one line from the file, which the recognition is based on Returns:a reader function

get_type()

Gets the type of the trace set.

Returns:type

number_of_traces()

Gets the number of traces held by the object.

Returns:number of traces

spikeTimeReader(path, no_traces, scale, t_length, freq, trace_type)

Not available yet! Reads a spike timing file from PyNN with 9 line of headers (the parameters are the same as in the Read function)

Returns:a dictionary object holding the content of the file

Note

If the given file is not accessible the program will abort.

Note

If the number of traces in the file and the corresponding parameter is not equal, a sizeError is raised.

Note

In the future, it will return a SpikeTimes object instead.

traceReader(path, no_traces, scale, t_length, freq, trace_type)

Reads a simple text file with data columns separated by ” ”. (the parameters are the same as in the Read function)

Returns:a trace object holding the content of the file

Note

If the given file is not accessible the program will abort.

Note

If the number of traces in the file and the corresponding parameter is not equal, a sizeError is raised.

traceReaderTime(path, no_traces, scale, t_length, freq, trace_type)

Reads a simple text file, containing time trace as well and data columns separated by “t”. (the parameters are the same as in the Read function)

Returns:a trace object holding the content of the file

Note

If the given file is not accessible the program will abort.

Note

If the number of traces in the file and the corresponding parameter is not equal, a sizeError is raised.

class optimizer.traceHandler.SpikeTimes(dictionary, trace_type='spikes')

Not in use! Stores spike times in dictionary indexed by the cell’s id.

Parameters:

• dictionary – the dictionary which contains the data
• trace_type – type of the trace (should be fixed to “spikes”)

class optimizer.traceHandler.Trace(no_traces, scale='milli', t_length=1000, freq=100, trace_type=None)

Trace set object. Stores a trace set of a given type with every relevant data.

Parameters:

• no_traces – number of traces held by the object
• scale – the unit of the data (required for conversions)
• t_length – length of the trace(s)
• freq – sampling frequency
• trace_type – type of the trace set

Attr:

data: the traces are contained in the attribute named data in the order they were in the input file

Note

The sampling rate should be uniform in the set.

Note

The length of the traces should be the same, or the length of the shortest one should be considered.

Note

If the type of the trace is not recognized, the program will abort. The recognized types are “voltage”, “current” and “other” (“spike” is not available yet).

Convert(hoc_obj)

Converts a hoc vector into a python list and stores it in the container.

Parameters:hoc_obj – a hoc vector object

GetTrace(index)

Returns the trace having the index index form the container. Always use this function to get a given trace as they are stored in a non intuitive way and direct access would probably cause errors.

Parameters:index – the index of the trace to get

Note

If the given index is out of range, a sizeError is raised.

Returns:the required trace

Print()

Prints the contained data. Created for debugging purpose.

SetTrace(d)

Adds the given trace to the container.

Parameters:d – list containing the trace

reScale(value)

Re-scales the given value based on the scale of the Trace object.

Parameters:value – the value to be rescaled Returns:the rescaled value

optimizer.traceHandler.real_range(start, step, end)

Not in use! Generates real values from the given range.

Parameters:

• start – begin of range
• step – step between the values
• end – the end of the range

Returns:

list of real values

exception optimizer.traceHandler.sizeError(message)

Bases: exceptions.Exception

Exception class used by the trace handling related objects.

Parameters:message – error message to be displayed

class optimizer.traceHandler.traceWriter(tr_object, full_path, comment='', flag_write=1, sep='n', flag_multi=0)

Bases: optimizer.traceHandler.Trace

Not used! Writes the content of the given trace object to the given file(s).

Parameters:

• tr_object – trace object which must have data attribute
• full_path – the path of the output file
• comment – some header information
• flag_write – indicates if the properties of the trace is written or not
• sep – data separator string
• flag_multi – indicates if the separate traces should be written into separate files

Write()

Performs the writing.

Note

If flag_multi was set to true, then the traces will be written to multiple files.