def extract_spike_variable(description):
cond = prepare_string(description['raw_spike'])
if len(cond) > 1:
Global.Global._print(description['raw_spike'])
Global._error('The spike condition must be a single expression')
translator = Equation('raw_spike_cond', cond[0].strip(), description)
raw_spike_code = translator.parse()
# Also store the variables used in the condition, as it may be needed for CUDA generation
spike_code_dependencies = translator.dependencies()
reset_desc = []
if 'raw_reset' in description.keys() and description['raw_reset']:
reset_desc = process_equations(description['raw_reset'])
for var in reset_desc:
translator = Equation(var['name'], var['eq'], description)
var['cpp'] = translator.parse()
var['dependencies'] = translator.dependencies()
return {
'spike_cond': raw_spike_code,
'spike_cond_dependencies': spike_code_dependencies,
'spike_reset': reset_desc
}
def extract_spike_variable(description):
cond = prepare_string(description['raw_spike'])
if len(cond) > 1:
Global.Global._print(description['raw_spike'])
Global._error('The spike condition must be a single expression')
translator = Equation('raw_spike_cond',
cond[0].strip(),
description)
raw_spike_code = translator.parse()
# Also store the variables used in the condition, as it may be needed for CUDA generation
spike_code_dependencies = translator.dependencies()
reset_desc = []
if 'raw_reset' in description.keys() and description['raw_reset']:
reset_desc = process_equations(description['raw_reset'])
for var in reset_desc:
translator = Equation(var['name'], var['eq'],
description)
var['cpp'] = translator.parse()
var['dependencies'] = translator.dependencies()
return { 'spike_cond': raw_spike_code,
'spike_cond_dependencies': spike_code_dependencies,
'spike_reset': reset_desc}
def extract_stop_condition(pop):
eq = pop['stop_condition']['eq']
pop['stop_condition']['type'] = 'any'
# Check the flags
split = eq.split(':')
if len(split) > 1: # flag given
eq = split[0]
flags = split[1].strip()
split = flags.split(' ')
for el in split:
if el.strip() == 'all':
pop['stop_condition']['type'] = 'all'
# Convert the expression
translator = Equation('stop_cond', eq, pop, type='cond')
code = translator.parse()
deps = translator.dependencies()
pop['stop_condition']['cpp'] = '(' + code + ')'
pop['stop_condition']['dependencies'] = deps
def extract_stop_condition(pop):
eq = pop['stop_condition']['eq']
pop['stop_condition']['type'] = 'any'
# Check the flags
split = eq.split(':')
if len(split) > 1: # flag given
eq = split[0]
flags = split[1].strip()
split = flags.split(' ')
for el in split:
if el.strip() == 'all':
pop['stop_condition']['type'] = 'all'
# Convert the expression
translator = Equation('stop_cond', eq,
pop,
type = 'cond')
code = translator.parse()
deps = translator.dependencies()
pop['stop_condition']['cpp'] = '(' + code + ')'
pop['stop_condition']['dependencies'] = deps
def analyse_neuron(neuron):
"""
Parses the structure and generates code snippets for the neuron type.
It returns a ``description`` dictionary with the following fields:
* 'object': 'neuron' by default, to distinguish it from 'synapse'
* 'type': either 'rate' or 'spiking'
* 'raw_parameters': provided field
* 'raw_equations': provided field
* 'raw_functions': provided field
* 'raw_reset': provided field
* 'raw_spike': provided field
* 'refractory': provided field
* 'parameters': list of parameters defined for the neuron type
* 'variables': list of variables defined for the neuron type
* 'functions': list of functions defined for the neuron type
* 'attributes': list of names of all parameters and variables
* 'local': list of names of parameters and variables which are local to each neuron
* 'global': list of names of parameters and variables which are global to the population
* 'targets': list of targets used in the equations
* 'random_distributions': list of random number generators used in the neuron equations
* 'global_operations': list of global operations (min/max/mean...) used in the equations (unused)
* 'spike': when defined, contains the equations of the spike conditions and reset.
Each parameter is a dictionary with the following elements:
* 'bounds': unused
* 'ctype': 'type of the parameter: 'float', 'double', 'int' or 'bool'
* 'eq': original equation in text format
* 'flags': list of flags provided after the :
* 'init': initial value
* 'locality': 'local' or 'global'
* 'name': name of the parameter
Each variable is a dictionary with the following elements:
* 'bounds': dictionary of bounds ('init', 'min', 'max') provided after the :
* 'cpp': C++ code snippet updating the variable
* 'ctype': type of the variable: 'float', 'double', 'int' or 'bool'
* 'dependencies': list of variable and parameter names on which the equation depends
* 'eq': original equation in text format
* 'flags': list of flags provided after the :
* 'init': initial value
* 'locality': 'local' or 'global'
* 'method': numericalmethod for ODEs
* 'name': name of the variable
* 'pre_loop': ODEs have a pre_loop term for precomputing dt/tau. dict with 'name' and 'value'. type must be inferred.
* 'switch': ODEs have a switch term
* 'transformed_eq': same as eq, except special terms (sums, rds) are replaced with a temporary name
* 'untouched': dictionary of special terms, with their new name as keys and replacement values as values.
The 'spike' element (when present) is a dictionary containing:
* 'spike_cond': the C++ code snippet containing the spike condition ("v%(local_index)s > v_T")
* 'spike_cond_dependencies': list of variables/parameters on which the spike condition depends
* 'spike_reset': a list of reset statements, each of them composed of :
* 'constraint': either '' or 'unless_refractory'
* 'cpp': C++ code snippet
* 'dependencies': list of variables on which the reset statement depends
* 'eq': original equation in text format
* 'name': name of the reset variable
"""
# Store basic information
description = {
'object': 'neuron',
'type': neuron.type,
'raw_parameters': neuron.parameters,
'raw_equations': neuron.equations,
'raw_functions': neuron.functions,
}
# Spiking neurons additionally store the spike condition, the reset statements and a refractory period
if neuron.type == 'spike':
description['raw_reset'] = neuron.reset
description['raw_spike'] = neuron.spike
description['raw_axon_spike'] = neuron.axon_spike
description['raw_axon_reset'] = neuron.axon_reset
description['refractory'] = neuron.refractory
# Extract parameters and variables names
parameters = extract_parameters(neuron.parameters, neuron.extra_values)
variables = extract_variables(neuron.equations)
description['parameters'] = parameters
description['variables'] = variables
# Make sure r is defined for rate-coded networks
from ANNarchy.extensions.bold.BoldModel import BoldModel
if isinstance(neuron, BoldModel):
found = False
for var in description['parameters'] + description['variables']:
if var['name'] == 'r':
found = True
if not found:
description['variables'].append({
'name': 'r',
'locality': 'local',
'bounds': {},
'ctype': config['precision'],
'init': 0.0,
'flags': [],
'eq': '',
'cpp': ""
})
elif neuron.type == 'rate':
for var in description['parameters'] + description['variables']:
if var['name'] == 'r':
break
else:
_error('Rate-coded neurons must define the variable "r".')
else: # spiking neurons define r by default, it contains the average FR if enabled
for var in description['parameters'] + description['variables']:
if var['name'] == 'r':
_error(
'Spiking neurons use the variable "r" for the average FR, use another name.'
)
description['variables'].append({
'name': 'r',
'locality': 'local',
'bounds': {},
'ctype': config['precision'],
'init': 0.0,
'flags': [],
'eq': '',
'cpp': ""
})
# Extract functions
functions = extract_functions(neuron.functions, False)
description['functions'] = functions
# Build lists of all attributes (param + var), which are local or global
attributes, local_var, global_var, _ = get_attributes(parameters,
variables,
neuron=True)
# Test if attributes are declared only once
if len(attributes) != len(list(set(attributes))):
_error('Attributes must be declared only once.', attributes)
# Store the attributes
description['attributes'] = attributes
description['local'] = local_var
description['semiglobal'] = [] # only for projections
description['global'] = global_var
# Extract all targets
targets = sorted(list(set(extract_targets(variables))))
description['targets'] = targets
if neuron.type == 'spike': # Add a default reset behaviour for conductances
for target in targets:
found = False
for var in description['variables']:
if var['name'] == 'g_' + target:
found = True
break
if not found:
description['variables'].append({
'name': 'g_' + target,
'locality': 'local',
'bounds': {},
'ctype': config['precision'],
'init': 0.0,
'flags': [],
'eq': 'g_' + target + ' = 0.0'
})
description['attributes'].append('g_' + target)
description['local'].append('g_' + target)
# Extract RandomDistribution objects
random_distributions = extract_randomdist(description)
description['random_distributions'] = random_distributions
# Extract the spike condition if any
if neuron.type == 'spike':
description['spike'] = extract_spike_variable(description)
description['axon_spike'] = extract_axon_spike_condition(description)
# Global operation TODO
description['global_operations'] = []
# The ODEs may be interdependent (implicit, midpoint), so they need to be passed explicitely to CoupledEquations
concurrent_odes = []
# Translate the equations to C++
for variable in description['variables']:
# Get the equation
eq = variable['transformed_eq']
if eq.strip() == "":
continue
# Special variables (sums, global operations, rd) are placed in untouched, so that Sympy ignores them
untouched = {}
# Dependencies must be gathered
dependencies = []
# Replace sum(target) with _sum_exc__[i]
for target in description['targets']:
# sum() is valid for all targets
eq = re.sub(r'(?P<pre>[^\w.])sum\(\)', r'\1sum(__all__)', eq)
# Replace sum(target) with __sum_target__
eq = re.sub('sum\(\s*' + target + '\s*\)',
'__sum_' + target + '__', eq)
untouched['__sum_' + target +
'__'] = '_sum_' + target + '%(local_index)s'
# Extract global operations
eq, untouched_globs, global_ops = extract_globalops_neuron(
variable['name'], eq, description)
# Add the untouched variables to the global list
for name, val in untouched_globs.items():
if not name in untouched.keys():
untouched[name] = val
description['global_operations'] += global_ops
# Extract if-then-else statements
eq, condition = extract_ite(variable['name'], eq, description)
# Find the numerical method if any
method = find_method(variable)
# Process the bounds
if 'min' in variable['bounds'].keys():
if isinstance(variable['bounds']['min'], str):
translator = Equation(variable['name'],
variable['bounds']['min'],
description,
type='return',
untouched=untouched)
variable['bounds']['min'] = translator.parse().replace(';', '')
dependencies += translator.dependencies()
if 'max' in variable['bounds'].keys():
if isinstance(variable['bounds']['max'], str):
translator = Equation(variable['name'],
variable['bounds']['max'],
description,
type='return',
untouched=untouched)
variable['bounds']['max'] = translator.parse().replace(';', '')
dependencies += translator.dependencies()
# Analyse the equation
if condition == []: # No if-then-else
translator = Equation(variable['name'],
eq,
description,
method=method,
untouched=untouched)
code = translator.parse()
dependencies += translator.dependencies()
else: # An if-then-else statement
code, deps = translate_ITE(variable['name'], eq, condition,
description, untouched)
dependencies += deps
# ODEs have a switch statement:
# double _r = (1.0 - r)/tau;
# r[i] += dt* _r;
# while direct assignments are one-liners:
# r[i] = 1.0
if isinstance(code, str):
pre_loop = {}
cpp_eq = code
switch = None
else: # ODE
pre_loop = code[0]
cpp_eq = code[1]
switch = code[2]
# Replace untouched variables with their original name
for prev, new in untouched.items():
if prev.startswith('g_'):
cpp_eq = re.sub(r'([^_]+)' + prev, r'\1' + new,
' ' + cpp_eq).strip()
if len(pre_loop) > 0:
pre_loop['value'] = re.sub(r'([^_]+)' + prev, new, ' ' +
pre_loop['value']).strip()
if switch:
switch = re.sub(r'([^_]+)' + prev, new,
' ' + switch).strip()
else:
cpp_eq = re.sub(prev, new, cpp_eq)
if len(pre_loop) > 0:
pre_loop['value'] = re.sub(prev, new, pre_loop['value'])
if switch:
switch = re.sub(prev, new, switch)
# Replace local functions
for f in description['functions']:
cpp_eq = re.sub(r'([^\w]*)' + f['name'] + '\(',
r'\1' + f['name'] + '(', ' ' + cpp_eq).strip()
# Store the result
variable[
'pre_loop'] = pre_loop # Things to be declared before the for loop (eg. dt)
variable['cpp'] = cpp_eq # the C++ equation
variable['switch'] = switch # switch value of ODE
variable['untouched'] = untouched # may be needed later
variable['method'] = method # may be needed later
variable['dependencies'] = list(
set(dependencies)) # may be needed later
# If the method is implicit or midpoint, the equations must be solved concurrently (depend on v[t+1])
if method in ['implicit', 'midpoint', 'runge-kutta4'
] and switch is not None:
concurrent_odes.append(variable)
# After all variables are processed, do it again if they are concurrent
if len(concurrent_odes) > 1:
solver = CoupledEquations(description, concurrent_odes)
new_eqs = solver.parse()
for idx, variable in enumerate(description['variables']):
for new_eq in new_eqs:
if variable['name'] == new_eq['name']:
description['variables'][idx] = new_eq
return description
def extract_structural_plasticity(statement, description):
# Extract flags
try:
eq, constraint = statement.rsplit(':', 1)
bounds, flags = extract_flags(constraint)
except:
eq = statement.strip()
bounds = {}
flags = []
# Extract RD
rd = None
for dist in available_distributions:
matches = re.findall('(?P<pre>[^\w.])' + dist + '\(([^()]+)\)', eq)
for l, v in matches:
# Check the arguments
arguments = v.split(',')
# Check the number of provided arguments
if len(arguments) < distributions_arguments[dist]:
Global._print(eq)
Global._error('The distribution ' + dist + ' requires ' +
str(distributions_arguments[dist]) +
'parameters')
elif len(arguments) > distributions_arguments[dist]:
Global._print(eq)
Global._error(
'Too many parameters provided to the distribution ' + dist)
# Process the arguments
processed_arguments = ""
for idx in range(len(arguments)):
try:
arg = float(arguments[idx])
except: # A global parameter
Global._print(eq)
Global._error(
'Random distributions for creating/pruning synapses must use foxed values.'
)
processed_arguments += str(arg)
if idx != len(arguments) - 1: # not the last one
processed_arguments += ', '
definition = distributions_equivalents[
dist] + '(' + processed_arguments + ')'
# Store its definition
if rd:
Global._print(eq)
Global._error(
'Only one random distribution per equation is allowed.')
rd = {
'name': 'rand_' + str(0),
'origin': dist + '(' + v + ')',
'dist': dist,
'definition': definition,
'args': processed_arguments,
'template': distributions_equivalents[dist]
}
if rd:
eq = eq.replace(rd['origin'], 'rd(rng)')
# Extract pre/post dependencies
eq, untouched, dependencies = extract_prepost('test', eq, description)
# Parse code
translator = Equation('test', eq, description, method='cond', untouched={})
code = translator.parse()
deps = translator.dependencies()
# Replace untouched variables with their original name
for prev, new in untouched.items():
code = code.replace(prev, new)
# Add new dependencies
for dep in dependencies['pre']:
description['dependencies']['pre'].append(dep)
for dep in dependencies['post']:
description['dependencies']['post'].append(dep)
return {
'eq': eq,
'cpp': code,
'bounds': bounds,
'flags': flags,
'rd': rd,
'dependencies': deps
}
def extract_structural_plasticity(statement, description):
# Extract flags
try:
eq, constraint = statement.rsplit(':', 1)
bounds, flags = extract_flags(constraint)
except:
eq = statement.strip()
bounds = {}
flags = []
# Extract RD
rd = None
for dist in available_distributions:
matches = re.findall('(?P<pre>[^\w.])'+dist+'\(([^()]+)\)', eq)
for l, v in matches:
# Check the arguments
arguments = v.split(',')
# Check the number of provided arguments
if len(arguments) < distributions_arguments[dist]:
Global._print(eq)
Global._error('The distribution ' + dist + ' requires ' + str(distributions_arguments[dist]) + 'parameters')
elif len(arguments) > distributions_arguments[dist]:
Global._print(eq)
Global._error('Too many parameters provided to the distribution ' + dist)
# Process the arguments
processed_arguments = ""
for idx in range(len(arguments)):
try:
arg = float(arguments[idx])
except: # A global parameter
Global._print(eq)
Global._error('Random distributions for creating/pruning synapses must use foxed values.')
processed_arguments += str(arg)
if idx != len(arguments)-1: # not the last one
processed_arguments += ', '
definition = distributions_equivalents[dist] + '(' + processed_arguments + ')'
# Store its definition
if rd:
Global._print(eq)
Global._error('Only one random distribution per equation is allowed.')
rd = {'name': 'rand_' + str(0) ,
'origin': dist+'('+v+')',
'dist': dist,
'definition': definition,
'args' : processed_arguments,
'template': distributions_equivalents[dist]}
if rd:
eq = eq.replace(rd['origin'], 'rd(rng)')
# Extract pre/post dependencies
eq, untouched, dependencies = extract_prepost('test', eq, description)
# Parse code
translator = Equation('test', eq,
description,
method = 'cond',
untouched = {})
code = translator.parse()
deps = translator.dependencies()
# Replace untouched variables with their original name
for prev, new in untouched.items():
code = code.replace(prev, new)
# Add new dependencies
for dep in dependencies['pre']:
description['dependencies']['pre'].append(dep)
for dep in dependencies['post']:
description['dependencies']['post'].append(dep)
return {'eq': eq, 'cpp': code, 'bounds': bounds, 'flags': flags, 'rd': rd, 'dependencies': deps}
def analyse_synapse(synapse):
"""
Parses the structure and generates code snippets for the synapse type.
It returns a ``description`` dictionary with the following fields:
* 'object': 'synapse' by default, to distinguish it from 'neuron'
* 'type': either 'rate' or 'spiking'
* 'raw_parameters': provided field
* 'raw_equations': provided field
* 'raw_functions': provided field
* 'raw_psp': provided field
* 'raw_pre_spike': provided field
* 'raw_post_spike': provided field
* 'parameters': list of parameters defined for the synapse type
* 'variables': list of variables defined for the synapse type
* 'functions': list of functions defined for the synapse type
* 'attributes': list of names of all parameters and variables
* 'local': list of names of parameters and variables which are local to each synapse
* 'semiglobal': list of names of parameters and variables which are local to each postsynaptic neuron
* 'global': list of names of parameters and variables which are global to the projection
* 'random_distributions': list of random number generators used in the neuron equations
* 'global_operations': list of global operations (min/max/mean...) used in the equations
* 'pre_global_operations': list of global operations (min/max/mean...) on the pre-synaptic population
* 'post_global_operations': list of global operations (min/max/mean...) on the post-synaptic population
* 'pre_spike': list of variables updated after a pre-spike event
* 'post_spike': list of variables updated after a post-spike event
* 'dependencies': dictionary ('pre', 'post') of lists of pre (resp. post) variables accessed by the synapse (used for delaying variables)
* 'psp': dictionary ('eq' and 'psp') for the psp code to be summed
* 'pruning' and 'creating': statements for structural plasticity
Each parameter is a dictionary with the following elements:
* 'bounds': unused
* 'ctype': 'type of the parameter: 'float', 'double', 'int' or 'bool'
* 'eq': original equation in text format
* 'flags': list of flags provided after the :
* 'init': initial value
* 'locality': 'local', 'semiglobal' or 'global'
* 'name': name of the parameter
Each variable is a dictionary with the following elements:
* 'bounds': dictionary of bounds ('init', 'min', 'max') provided after the :
* 'cpp': C++ code snippet updating the variable
* 'ctype': type of the variable: 'float', 'double', 'int' or 'bool'
* 'dependencies': list of variable and parameter names on which the equation depends
* 'eq': original equation in text format
* 'flags': list of flags provided after the :
* 'init': initial value
* 'locality': 'local', 'semiglobal' or 'global'
* 'method': numericalmethod for ODEs
* 'name': name of the variable
* 'pre_loop': ODEs have a pre_loop term for precomputing dt/tau
* 'switch': ODEs have a switch term
* 'transformed_eq': same as eq, except special terms (sums, rds) are replaced with a temporary name
* 'untouched': dictionary of special terms, with their new name as keys and replacement values as values.
"""
# Store basic information
description = {
'object': 'synapse',
'type': synapse.type,
'raw_parameters': synapse.parameters,
'raw_equations': synapse.equations,
'raw_functions': synapse.functions
}
# Psps is what is actually summed over the incoming weights
if synapse.psp:
description['raw_psp'] = synapse.psp
elif synapse.type == 'rate':
description['raw_psp'] = "w*pre.r"
# Spiking synapses additionally store pre_spike and post_spike
if synapse.type == 'spike':
description['raw_pre_spike'] = synapse.pre_spike
description['raw_post_spike'] = synapse.post_spike
# Extract parameters and variables names
parameters = extract_parameters(synapse.parameters, synapse.extra_values)
variables = extract_variables(synapse.equations)
# Extract functions
functions = extract_functions(synapse.functions, False)
# Check the presence of w
description['plasticity'] = False
for var in parameters + variables:
if var['name'] == 'w':
break
else:
parameters.append(
{
'name': 'w', 'bounds': {}, 'ctype': config['precision'],
'init': 0.0, 'flags': [], 'eq': 'w=0.0', 'locality': 'local'
}
)
# Find out a plasticity rule
for var in variables:
if var['name'] == 'w':
description['plasticity'] = True
break
# Build lists of all attributes (param+var), which are local or global
attributes, local_var, global_var, semiglobal_var = get_attributes(parameters, variables, neuron=False)
# Test if attributes are declared only once
if len(attributes) != len(list(set(attributes))):
_error('Attributes must be declared only once.', attributes)
# Add this info to the description
description['parameters'] = parameters
description['variables'] = variables
description['functions'] = functions
description['attributes'] = attributes
description['local'] = local_var
description['semiglobal'] = semiglobal_var
description['global'] = global_var
description['global_operations'] = []
# Lists of global operations needed at the pre and post populations
description['pre_global_operations'] = []
description['post_global_operations'] = []
# Extract RandomDistribution objects
description['random_distributions'] = extract_randomdist(description)
# Extract event-driven info
if description['type'] == 'spike':
# pre_spike event
description['pre_spike'] = extract_pre_spike_variable(description)
for var in description['pre_spike']:
if var['name'] in ['g_target']: # Already dealt with
continue
for avar in description['variables']:
if var['name'] == avar['name']:
break
else: # not defined already
description['variables'].append(
{'name': var['name'], 'bounds': var['bounds'], 'ctype': var['ctype'], 'init': var['init'],
'locality': var['locality'],
'flags': [], 'transformed_eq': '', 'eq': '',
'cpp': '', 'switch': '', 're_loop': '',
'untouched': '', 'method':'explicit'}
)
description['local'].append(var['name'])
description['attributes'].append(var['name'])
# post_spike event
description['post_spike'] = extract_post_spike_variable(description)
for var in description['post_spike']:
if var['name'] in ['g_target', 'w']: # Already dealt with
continue
for avar in description['variables']:
if var['name'] == avar['name']:
break
else: # not defined already
description['variables'].append(
{'name': var['name'], 'bounds': var['bounds'], 'ctype': var['ctype'], 'init': var['init'],
'locality': var['locality'],
'flags': [], 'transformed_eq': '', 'eq': '',
'cpp': '', 'switch': '', 'untouched': '', 'method':'explicit'}
)
description['local'].append(var['name'])
description['attributes'].append(var['name'])
# Variables names for the parser which should be left untouched
untouched = {}
description['dependencies'] = {'pre': [], 'post': []}
# The ODEs may be interdependent (implicit, midpoint), so they need to be passed explicitely to CoupledEquations
concurrent_odes = []
# Iterate over all variables
for variable in description['variables']:
# Equation
eq = variable['transformed_eq']
if eq.strip() == '':
continue
# Dependencies must be gathered
dependencies = []
# Extract global operations
eq, untouched_globs, global_ops = extract_globalops_synapse(variable['name'], eq, description)
description['pre_global_operations'] += global_ops['pre']
description['post_global_operations'] += global_ops['post']
# Remove doubled entries
description['pre_global_operations'] = [i for n, i in enumerate(description['pre_global_operations']) if i not in description['pre_global_operations'][n + 1:]]
description['post_global_operations'] = [i for n, i in enumerate(description['post_global_operations']) if i not in description['post_global_operations'][n + 1:]]
# Extract pre- and post_synaptic variables
eq, untouched_var, prepost_dependencies = extract_prepost(variable['name'], eq, description)
# Store the pre-post dependencies at the synapse level
description['dependencies']['pre'] += prepost_dependencies['pre']
description['dependencies']['post'] += prepost_dependencies['post']
# and also on the variable for checking
variable['prepost_dependencies'] = prepost_dependencies
# Extract if-then-else statements
eq, condition = extract_ite(variable['name'], eq, description)
# Add the untouched variables to the global list
for name, val in untouched_globs.items():
if not name in untouched.keys():
untouched[name] = val
for name, val in untouched_var.items():
if not name in untouched.keys():
untouched[name] = val
# Save the tranformed equation
variable['transformed_eq'] = eq
# Find the numerical method if any
method = find_method(variable)
# Process the bounds
if 'min' in variable['bounds'].keys():
if isinstance(variable['bounds']['min'], str):
translator = Equation(variable['name'], variable['bounds']['min'],
description,
type = 'return',
untouched = untouched.keys())
variable['bounds']['min'] = translator.parse().replace(';', '')
dependencies += translator.dependencies()
if 'max' in variable['bounds'].keys():
if isinstance(variable['bounds']['max'], str):
translator = Equation(variable['name'], variable['bounds']['max'],
description,
type = 'return',
untouched = untouched.keys())
variable['bounds']['max'] = translator.parse().replace(';', '')
dependencies += translator.dependencies()
# Analyse the equation
if condition == []: # Call Equation
translator = Equation(variable['name'], eq,
description,
method = method,
untouched = untouched.keys())
code = translator.parse()
dependencies += translator.dependencies()
else: # An if-then-else statement
code, deps = translate_ITE(variable['name'], eq, condition, description,
untouched)
dependencies += deps
if isinstance(code, str):
pre_loop = {}
cpp_eq = code
switch = None
else: # ODE
pre_loop = code[0]
cpp_eq = code[1]
switch = code[2]
# Replace untouched variables with their original name
for prev, new in untouched.items():
cpp_eq = cpp_eq.replace(prev, new)
# Replace local functions
for f in description['functions']:
cpp_eq = re.sub(r'([^\w]*)'+f['name']+'\(', r'\1'+ f['name'] + '(', ' ' + cpp_eq).strip()
# Store the result
variable['pre_loop'] = pre_loop # Things to be declared before the for loop (eg. dt)
variable['cpp'] = cpp_eq # the C++ equation
variable['switch'] = switch # switch value id ODE
variable['untouched'] = untouched # may be needed later
variable['method'] = method # may be needed later
variable['dependencies'] = dependencies
# If the method is implicit or midpoint, the equations must be solved concurrently (depend on v[t+1])
if method in ['implicit', 'midpoint'] and switch is not None:
concurrent_odes.append(variable)
# After all variables are processed, do it again if they are concurrent
if len(concurrent_odes) > 1 :
solver = CoupledEquations(description, concurrent_odes)
new_eqs = solver.parse()
for idx, variable in enumerate(description['variables']):
for new_eq in new_eqs:
if variable['name'] == new_eq['name']:
description['variables'][idx] = new_eq
# Translate the psp code if any
if 'raw_psp' in description.keys():
psp = {'eq' : description['raw_psp'].strip() }
# Extract global operations
eq, untouched_globs, global_ops = extract_globalops_synapse('psp', " " + psp['eq'] + " ", description)
description['pre_global_operations'] += global_ops['pre']
description['post_global_operations'] += global_ops['post']
# Replace pre- and post_synaptic variables
eq, untouched, prepost_dependencies = extract_prepost('psp', eq, description)
description['dependencies']['pre'] += prepost_dependencies['pre']
description['dependencies']['post'] += prepost_dependencies['post']
for name, val in untouched_globs.items():
if not name in untouched.keys():
untouched[name] = val
# Extract if-then-else statements
eq, condition = extract_ite('psp', eq, description, split=False)
# Analyse the equation
if condition == []:
translator = Equation('psp', eq,
description,
method = 'explicit',
untouched = untouched.keys(),
type='return')
code = translator.parse()
deps = translator.dependencies()
else:
code, deps = translate_ITE('psp', eq, condition, description, untouched)
# Replace untouched variables with their original name
for prev, new in untouched.items():
code = code.replace(prev, new)
# Store the result
psp['cpp'] = code
psp['dependencies'] = deps
description['psp'] = psp
# Process event-driven info
if description['type'] == 'spike':
for variable in description['pre_spike'] + description['post_spike']:
# Find plasticity
if variable['name'] == 'w':
description['plasticity'] = True
# Retrieve the equation
eq = variable['eq']
# Extract if-then-else statements
eq, condition = extract_ite(variable['name'], eq, description)
# Extract pre- and post_synaptic variables
eq, untouched, prepost_dependencies = extract_prepost(variable['name'], eq, description)
# Update dependencies
description['dependencies']['pre'] += prepost_dependencies['pre']
description['dependencies']['post'] += prepost_dependencies['post']
# and also on the variable for checking
variable['prepost_dependencies'] = prepost_dependencies
# Analyse the equation
dependencies = []
if condition == []:
translator = Equation(variable['name'],
eq,
description,
method = 'explicit',
untouched = untouched)
code = translator.parse()
dependencies += translator.dependencies()
else:
code, deps = translate_ITE(variable['name'], eq, condition, description, untouched)
dependencies += deps
if isinstance(code, list): # an ode in a pre/post statement
Global._print(eq)
if variable in description['pre_spike']:
Global._error('It is forbidden to use ODEs in a pre_spike term.')
elif variable in description['posz_spike']:
Global._error('It is forbidden to use ODEs in a post_spike term.')
else:
Global._error('It is forbidden to use ODEs here.')
# Replace untouched variables with their original name
for prev, new in untouched.items():
code = code.replace(prev, new)
# Process the bounds
if 'min' in variable['bounds'].keys():
if isinstance(variable['bounds']['min'], str):
translator = Equation(
variable['name'],
variable['bounds']['min'],
description,
type = 'return',
untouched = untouched )
variable['bounds']['min'] = translator.parse().replace(';', '')
dependencies += translator.dependencies()
if 'max' in variable['bounds'].keys():
if isinstance(variable['bounds']['max'], str):
translator = Equation(
variable['name'],
variable['bounds']['max'],
description,
type = 'return',
untouched = untouched)
variable['bounds']['max'] = translator.parse().replace(';', '')
dependencies += translator.dependencies()
# Store the result
variable['cpp'] = code # the C++ equation
variable['dependencies'] = dependencies
# Structural plasticity
if synapse.pruning:
description['pruning'] = extract_structural_plasticity(synapse.pruning, description)
if synapse.creating:
description['creating'] = extract_structural_plasticity(synapse.creating, description)
return description
def analyse_synapse(synapse):
"""
Parses the structure and generates code snippets for the synapse type.
It returns a ``description`` dictionary with the following fields:
* 'object': 'synapse' by default, to distinguish it from 'neuron'
* 'type': either 'rate' or 'spiking'
* 'raw_parameters': provided field
* 'raw_equations': provided field
* 'raw_functions': provided field
* 'raw_psp': provided field
* 'raw_pre_spike': provided field
* 'raw_post_spike': provided field
* 'parameters': list of parameters defined for the synapse type
* 'variables': list of variables defined for the synapse type
* 'functions': list of functions defined for the synapse type
* 'attributes': list of names of all parameters and variables
* 'local': list of names of parameters and variables which are local to each synapse
* 'semiglobal': list of names of parameters and variables which are local to each postsynaptic neuron
* 'global': list of names of parameters and variables which are global to the projection
* 'random_distributions': list of random number generators used in the neuron equations
* 'global_operations': list of global operations (min/max/mean...) used in the equations
* 'pre_global_operations': list of global operations (min/max/mean...) on the pre-synaptic population
* 'post_global_operations': list of global operations (min/max/mean...) on the post-synaptic population
* 'pre_spike': list of variables updated after a pre-spike event
* 'post_spike': list of variables updated after a post-spike event
* 'dependencies': dictionary ('pre', 'post') of lists of pre (resp. post) variables accessed by the synapse (used for delaying variables)
* 'psp': dictionary ('eq' and 'psp') for the psp code to be summed
* 'pruning' and 'creating': statements for structural plasticity
Each parameter is a dictionary with the following elements:
* 'bounds': unused
* 'ctype': 'type of the parameter: 'float', 'double', 'int' or 'bool'
* 'eq': original equation in text format
* 'flags': list of flags provided after the :
* 'init': initial value
* 'locality': 'local', 'semiglobal' or 'global'
* 'name': name of the parameter
Each variable is a dictionary with the following elements:
* 'bounds': dictionary of bounds ('init', 'min', 'max') provided after the :
* 'cpp': C++ code snippet updating the variable
* 'ctype': type of the variable: 'float', 'double', 'int' or 'bool'
* 'dependencies': list of variable and parameter names on which the equation depends
* 'eq': original equation in text format
* 'flags': list of flags provided after the :
* 'init': initial value
* 'locality': 'local', 'semiglobal' or 'global'
* 'method': numericalmethod for ODEs
* 'name': name of the variable
* 'pre_loop': ODEs have a pre_loop term for precomputing dt/tau
* 'switch': ODEs have a switch term
* 'transformed_eq': same as eq, except special terms (sums, rds) are replaced with a temporary name
* 'untouched': dictionary of special terms, with their new name as keys and replacement values as values.
"""
# Store basic information
description = {
'object': 'synapse',
'type': synapse.type,
'raw_parameters': synapse.parameters,
'raw_equations': synapse.equations,
'raw_functions': synapse.functions
}
# Psps is what is actually summed over the incoming weights
if synapse.psp:
description['raw_psp'] = synapse.psp
elif synapse.type == 'rate':
description['raw_psp'] = "w*pre.r"
# Spiking synapses additionally store pre_spike and post_spike
if synapse.type == 'spike':
description['raw_pre_spike'] = synapse.pre_spike
description['raw_post_spike'] = synapse.post_spike
# Extract parameters and variables names
parameters = extract_parameters(synapse.parameters, synapse.extra_values)
variables = extract_variables(synapse.equations)
# Extract functions
functions = extract_functions(synapse.functions, False)
# Check the presence of w
description['plasticity'] = False
for var in parameters + variables:
if var['name'] == 'w':
break
else:
parameters.append({
'name': 'w',
'bounds': {},
'ctype': config['precision'],
'init': 0.0,
'flags': [],
'eq': 'w=0.0',
'locality': 'local'
})
# Find out a plasticity rule
for var in variables:
if var['name'] == 'w':
description['plasticity'] = True
break
# Build lists of all attributes (param+var), which are local or global
attributes, local_var, global_var, semiglobal_var = get_attributes(
parameters, variables, neuron=False)
# Test if attributes are declared only once
if len(attributes) != len(list(set(attributes))):
_error('Attributes must be declared only once.', attributes)
# Add this info to the description
description['parameters'] = parameters
description['variables'] = variables
description['functions'] = functions
description['attributes'] = attributes
description['local'] = local_var
description['semiglobal'] = semiglobal_var
description['global'] = global_var
description['global_operations'] = []
# Lists of global operations needed at the pre and post populations
description['pre_global_operations'] = []
description['post_global_operations'] = []
# Extract RandomDistribution objects
description['random_distributions'] = extract_randomdist(description)
# Extract event-driven info
if description['type'] == 'spike':
# pre_spike event
description['pre_spike'] = extract_pre_spike_variable(description)
for var in description['pre_spike']:
if var['name'] in ['g_target']: # Already dealt with
continue
for avar in description['variables']:
if var['name'] == avar['name']:
break
else: # not defined already
description['variables'].append({
'name': var['name'],
'bounds': var['bounds'],
'ctype': var['ctype'],
'init': var['init'],
'locality': var['locality'],
'flags': [],
'transformed_eq': '',
'eq': '',
'cpp': '',
'switch': '',
're_loop': '',
'untouched': '',
'method': 'explicit'
})
description['local'].append(var['name'])
description['attributes'].append(var['name'])
# post_spike event
description['post_spike'] = extract_post_spike_variable(description)
for var in description['post_spike']:
if var['name'] in ['g_target', 'w']: # Already dealt with
continue
for avar in description['variables']:
if var['name'] == avar['name']:
break
else: # not defined already
description['variables'].append({
'name': var['name'],
'bounds': var['bounds'],
'ctype': var['ctype'],
'init': var['init'],
'locality': var['locality'],
'flags': [],
'transformed_eq': '',
'eq': '',
'cpp': '',
'switch': '',
'untouched': '',
'method': 'explicit'
})
description['local'].append(var['name'])
description['attributes'].append(var['name'])
# Variables names for the parser which should be left untouched
untouched = {}
description['dependencies'] = {'pre': [], 'post': []}
# The ODEs may be interdependent (implicit, midpoint), so they need to be passed explicitely to CoupledEquations
concurrent_odes = []
# Iterate over all variables
for variable in description['variables']:
# Equation
eq = variable['transformed_eq']
if eq.strip() == '':
continue
# Dependencies must be gathered
dependencies = []
# Extract global operations
eq, untouched_globs, global_ops = extract_globalops_synapse(
variable['name'], eq, description)
description['pre_global_operations'] += global_ops['pre']
description['post_global_operations'] += global_ops['post']
# Remove doubled entries
description['pre_global_operations'] = [
i for n, i in enumerate(description['pre_global_operations'])
if i not in description['pre_global_operations'][n + 1:]
]
description['post_global_operations'] = [
i for n, i in enumerate(description['post_global_operations'])
if i not in description['post_global_operations'][n + 1:]
]
# Extract pre- and post_synaptic variables
eq, untouched_var, prepost_dependencies = extract_prepost(
variable['name'], eq, description)
# Store the pre-post dependencies at the synapse level
description['dependencies']['pre'] += prepost_dependencies['pre']
description['dependencies']['post'] += prepost_dependencies['post']
# and also on the variable for checking
variable['prepost_dependencies'] = prepost_dependencies
# Extract if-then-else statements
eq, condition = extract_ite(variable['name'], eq, description)
# Add the untouched variables to the global list
for name, val in untouched_globs.items():
if not name in untouched.keys():
untouched[name] = val
for name, val in untouched_var.items():
if not name in untouched.keys():
untouched[name] = val
# Save the tranformed equation
variable['transformed_eq'] = eq
# Find the numerical method if any
method = find_method(variable)
# Process the bounds
if 'min' in variable['bounds'].keys():
if isinstance(variable['bounds']['min'], str):
translator = Equation(variable['name'],
variable['bounds']['min'],
description,
type='return',
untouched=untouched.keys())
variable['bounds']['min'] = translator.parse().replace(';', '')
dependencies += translator.dependencies()
if 'max' in variable['bounds'].keys():
if isinstance(variable['bounds']['max'], str):
translator = Equation(variable['name'],
variable['bounds']['max'],
description,
type='return',
untouched=untouched.keys())
variable['bounds']['max'] = translator.parse().replace(';', '')
dependencies += translator.dependencies()
# Analyse the equation
if condition == []: # Call Equation
translator = Equation(variable['name'],
eq,
description,
method=method,
untouched=untouched.keys())
code = translator.parse()
dependencies += translator.dependencies()
else: # An if-then-else statement
code, deps = translate_ITE(variable['name'], eq, condition,
description, untouched)
dependencies += deps
if isinstance(code, str):
pre_loop = {}
cpp_eq = code
switch = None
else: # ODE
pre_loop = code[0]
cpp_eq = code[1]
switch = code[2]
# Replace untouched variables with their original name
for prev, new in untouched.items():
cpp_eq = cpp_eq.replace(prev, new)
# Replace local functions
for f in description['functions']:
cpp_eq = re.sub(r'([^\w]*)' + f['name'] + '\(',
r'\1' + f['name'] + '(', ' ' + cpp_eq).strip()
# Store the result
variable[
'pre_loop'] = pre_loop # Things to be declared before the for loop (eg. dt)
variable['cpp'] = cpp_eq # the C++ equation
variable['switch'] = switch # switch value id ODE
variable['untouched'] = untouched # may be needed later
variable['method'] = method # may be needed later
variable['dependencies'] = dependencies
# If the method is implicit or midpoint, the equations must be solved concurrently (depend on v[t+1])
if method in ['implicit', 'midpoint'] and switch is not None:
concurrent_odes.append(variable)
# After all variables are processed, do it again if they are concurrent
if len(concurrent_odes) > 1:
solver = CoupledEquations(description, concurrent_odes)
new_eqs = solver.parse()
for idx, variable in enumerate(description['variables']):
for new_eq in new_eqs:
if variable['name'] == new_eq['name']:
description['variables'][idx] = new_eq
# Translate the psp code if any
if 'raw_psp' in description.keys():
psp = {'eq': description['raw_psp'].strip()}
# Extract global operations
eq, untouched_globs, global_ops = extract_globalops_synapse(
'psp', " " + psp['eq'] + " ", description)
description['pre_global_operations'] += global_ops['pre']
description['post_global_operations'] += global_ops['post']
# Replace pre- and post_synaptic variables
eq, untouched, prepost_dependencies = extract_prepost(
'psp', eq, description)
description['dependencies']['pre'] += prepost_dependencies['pre']
description['dependencies']['post'] += prepost_dependencies['post']
for name, val in untouched_globs.items():
if not name in untouched.keys():
untouched[name] = val
# Extract if-then-else statements
eq, condition = extract_ite('psp', eq, description, split=False)
# Analyse the equation
if condition == []:
translator = Equation('psp',
eq,
description,
method='explicit',
untouched=untouched.keys(),
type='return')
code = translator.parse()
deps = translator.dependencies()
else:
code, deps = translate_ITE('psp', eq, condition, description,
untouched)
# Replace untouched variables with their original name
for prev, new in untouched.items():
code = code.replace(prev, new)
# Store the result
psp['cpp'] = code
psp['dependencies'] = deps
description['psp'] = psp
# Process event-driven info
if description['type'] == 'spike':
for variable in description['pre_spike'] + description['post_spike']:
# Find plasticity
if variable['name'] == 'w':
description['plasticity'] = True
# Retrieve the equation
eq = variable['eq']
# Extract if-then-else statements
eq, condition = extract_ite(variable['name'], eq, description)
# Extract pre- and post_synaptic variables
eq, untouched, prepost_dependencies = extract_prepost(
variable['name'], eq, description)
# Update dependencies
description['dependencies']['pre'] += prepost_dependencies['pre']
description['dependencies']['post'] += prepost_dependencies['post']
# and also on the variable for checking
variable['prepost_dependencies'] = prepost_dependencies
# Analyse the equation
dependencies = []
if condition == []:
translator = Equation(variable['name'],
eq,
description,
method='explicit',
untouched=untouched)
code = translator.parse()
dependencies += translator.dependencies()
else:
code, deps = translate_ITE(variable['name'], eq, condition,
description, untouched)
dependencies += deps
if isinstance(code, list): # an ode in a pre/post statement
Global._print(eq)
if variable in description['pre_spike']:
Global._error(
'It is forbidden to use ODEs in a pre_spike term.')
elif variable in description['posz_spike']:
Global._error(
'It is forbidden to use ODEs in a post_spike term.')
else:
Global._error('It is forbidden to use ODEs here.')
# Replace untouched variables with their original name
for prev, new in untouched.items():
code = code.replace(prev, new)
# Process the bounds
if 'min' in variable['bounds'].keys():
if isinstance(variable['bounds']['min'], str):
translator = Equation(variable['name'],
variable['bounds']['min'],
description,
type='return',
untouched=untouched)
variable['bounds']['min'] = translator.parse().replace(
';', '')
dependencies += translator.dependencies()
if 'max' in variable['bounds'].keys():
if isinstance(variable['bounds']['max'], str):
translator = Equation(variable['name'],
variable['bounds']['max'],
description,
type='return',
untouched=untouched)
variable['bounds']['max'] = translator.parse().replace(
';', '')
dependencies += translator.dependencies()
# Store the result
variable['cpp'] = code # the C++ equation
variable['dependencies'] = dependencies
# Structural plasticity
if synapse.pruning:
description['pruning'] = extract_structural_plasticity(
synapse.pruning, description)
if synapse.creating:
description['creating'] = extract_structural_plasticity(
synapse.creating, description)
return description