def _generate_synapse_models(net_id):
txt = """
# Synapse models
"""
for idx, synapse in enumerate(Global._objects['synapses']):
# Do not document default synapses
if synapse.name == "-":
continue
# Find a name for the synapse
synapse_name = "Synapse " + str(synapse._rk_synapses_type) if synapse.name in Synapse._default_names.values() else synapse.name
# Description
description = synapse.short_description
if description == None:
description = "Spiking synapse." if synapse.type == 'spike' else 'Rate-coded synapse'
# Parameters
parameters = extract_parameters(synapse.parameters, synapse.extra_values)
parameters_list = [
["$" + LatexParser._latexify_name(param['name'], []) + "$", param['init'], _adapt_locality_synapse(param['locality']), param['ctype']]
for param in parameters]
parameters_headers = ["Name", "Default value", "Locality", "Type"]
parameters_table = _make_table(parameters_headers, parameters_list)
if len(parameters) == 0:
parameters_table = "$$\\varnothing$$"
# Generate the code for the equations
psp, variables, pre_desc, post_desc = LatexParser._process_synapse_equations(synapse)
eqs = _process_variables(variables, neuron = False)
# PSP
if synapse.type == "rate":
psp = """
**Weighted sum:**
$$%(transmission)s$$
""" % {'transmission': psp}
elif synapse.type == "spike" and psp != "":
psp = """
**Continuous transmission:**
$$%(transmission)s$$
""" % {'transmission': psp}
else:
psp = ""
# Pre- and post-events
if synapse.type == "spike":
if len(pre_desc) > 0:
eqs += """
**Pre-synaptic event at $t_\\text{pre} + d$:**
"""
for pre in pre_desc:
eqs += "$$"+pre+"$$\n"
if len(post_desc) > 0:
eqs += """
**Post-synaptic event at $t_\\text{post}$:**
"""
for post in post_desc:
eqs += "$$"+post+"$$\n"
# Finalize the template
txt += synapse_tpl % { 'name': synapse_name,
'description': description,
'psp': psp,
'parameters': parameters_table,
'eqs': eqs}
return txt
def _generate_synapse_models(net_id):
firstsynapse = ""
synapses = ""
firstsynapse = "\\hdr{2}{E}{Synapse Models}\\\\ \\hline"
synapse_tpl = """
\\noindent
\\begin{tabularx}{\\linewidth}{|p{0.15\\linewidth}|X|}\\hline
%(firstsynapse)s
\\textbf{Name} & %(name)s \\\\ \\hline
\\textbf{Type} & %(description)s\\\\ \\hline
%(psp)s
%(variables)s
%(preevent)s
%(postevent)s
%(functions)s
\\end{tabularx}
\\vspace{2ex}
"""
for idx, synapse in enumerate(Global._objects['synapses']):
# Do not document default synapses
if synapse.name == "-":
continue
# Find a name for the synapse
if synapse.name in Synapse._default_names.values(): # name not set
synapse_name = "Synapse " + str(synapse._rk_synapses_type)
else:
synapse_name = synapse.name
# Generate the code for the equations
psp, variables, pre_desc, post_desc = LatexParser._process_synapse_equations(synapse)
eqs = ""
for var in variables:
eqs += """
\\begin{dmath*}
%(eq)s
\\end{dmath*}
""" % {'eq': var['latex']}
variables_eqs = """
%(eqs)s
\\\\ \\hline
""" % {'eqs': eqs}
# Synaptic variables
variables = """
\\textbf{Equations} & %(variables)s
\\\\ \\hline""" % {'variables':eqs} if eqs != "" else ""
# PSP
if psp != "":
psp_code = """
\\textbf{PSP} & \\begin{dmath*}
%(psp)s
\\end{dmath*}
\\\\ \\hline""" % {'psp': psp}
else:
psp_code = ""
# Spiking neurons have extra fields for the event-driven
if synapse.type == 'spike':
if len(pre_desc) > 0:
txt_pre = ""
for l in pre_desc:
txt_pre += """
\\begin{dmath*}
%(eq)s
\\end{dmath*}
""" % {'eq': l}
preevent = """
\\textbf{Pre-synaptic event} &
%(preevent)s
\\\\ \\hline
""" % {'preevent': txt_pre}
else:
preevent = ""
if len(post_desc) > 0:
txt_post = ""
for l in post_desc:
txt_post += """
\\begin{dmath*}
%(eq)s
\\end{dmath*}
""" % {'eq': l}
postevent = """
\\textbf{Post-synaptic event} &
%(postevent)s
\\\\ \\hline
""" % {'postevent': txt_post}
else:
postevent = ""
else:
preevent = ""
postevent = ""
# Possible functions
functions = ""
if not synapse.functions == None:
functions = """
\\textbf{Functions} &
%(functions)s
\\\\ \\hline
""" % {'functions': LatexParser._process_functions(synapse.functions)}
# Build the dictionary
desc = {
'name': synapse_name,
'description': synapse.short_description,
'firstsynapse': firstsynapse if idx == 0 else "",
'variables': variables,
'psp': psp_code,
'preevent': preevent,
'postevent': postevent,
'functions': functions
}
# Generate the code
synapses += synapse_tpl % desc
return synapses
def _generate_synapse_models(net_id):
firstsynapse = ""
synapses = ""
firstsynapse = "\\hdr{2}{E}{Synapse Models}\\\\ \\hline"
synapse_tpl = """
\\noindent
\\begin{tabularx}{\\linewidth}{|p{0.15\\linewidth}|X|}\\hline
%(firstsynapse)s
\\textbf{Name} & %(name)s \\\\ \\hline
\\textbf{Type} & %(description)s\\\\ \\hline
%(psp)s
%(variables)s
%(preevent)s
%(postevent)s
%(functions)s
\\end{tabularx}
\\vspace{2ex}
"""
for idx, synapse in enumerate(Global._objects['synapses']):
# Do not document default synapses
if synapse.name == "-":
continue
# Find a name for the synapse
if synapse.name in Synapse._default_names.values(): # name not set
synapse_name = "Synapse " + str(synapse._rk_synapses_type)
else:
synapse_name = synapse.name
# Generate the code for the equations
psp, variables, pre_desc, post_desc = LatexParser._process_synapse_equations(synapse)
eqs = ""
for var in variables:
eqs += """
\\begin{dmath*}
%(eq)s
\\end{dmath*}
""" % {'eq': var['latex']}
variables_eqs = """
%(eqs)s
\\\\ \\hline
""" % {'eqs': eqs}
# Synaptic variables
variables = """
\\textbf{Equations} & %(variables)s
\\\\ \\hline""" % {'variables':eqs} if eqs != "" else ""
# PSP
if psp != "":
psp_code = """
\\textbf{PSP} & \\begin{dmath*}
%(psp)s
\\end{dmath*}
\\\\ \\hline""" % {'psp': psp}
else:
psp_code = ""
# Spiking neurons have extra fields for the event-driven
if synapse.type == 'spike':
if len(pre_desc) > 0:
txt_pre = ""
for l in pre_desc:
txt_pre += """
\\begin{dmath*}
%(eq)s
\\end{dmath*}
""" % {'eq': l}
preevent = """
\\textbf{Pre-synaptic event} &
%(preevent)s
\\\\ \\hline
""" % {'preevent': txt_pre}
else:
preevent = ""
if len(post_desc) > 0:
txt_post = ""
for l in post_desc:
txt_post += """
\\begin{dmath*}
%(eq)s
\\end{dmath*}
""" % {'eq': l}
postevent = """
\\textbf{Post-synaptic event} &
%(postevent)s
\\\\ \\hline
""" % {'postevent': txt_post}
else:
postevent = ""
else:
preevent = ""
postevent = ""
# Possible functions
functions = ""
if not synapse.functions == None:
functions = """
\\textbf{Functions} &
%(functions)s
\\\\ \\hline
""" % {'functions': LatexParser._process_functions(synapse.functions)}
# Build the dictionary
desc = {
'name': synapse_name,
'description': synapse.short_description,
'firstsynapse': firstsynapse if idx == 0 else "",
'variables': variables,
'psp': psp_code,
'preevent': preevent,
'postevent': postevent,
'functions': functions
}
# Generate the code
synapses += synapse_tpl % desc
return synapses
def _generate_synapse_models(net_id):
txt = """
# Synapse models
"""
for idx, synapse in enumerate(Global._objects['synapses']):
# Do not document default synapses
if synapse.name == "-":
continue
# Find a name for the synapse
synapse_name = "Synapse " + str(synapse._rk_synapses_type) if synapse.name in Synapse._default_names.values() else synapse.name
# Description
description = synapse.short_description
if description == None:
description = "Spiking synapse." if synapse.type == 'spike' else 'Rate-coded synapse'
# Parameters
parameters = extract_parameters(synapse.parameters, synapse.extra_values)
parameters_list = [
["$" + LatexParser._latexify_name(param['name'], []) + "$", param['init'], _adapt_locality_synapse(param['locality']), param['ctype']]
for param in parameters]
parameters_headers = ["Name", "Default value", "Locality", "Type"]
parameters_table = _make_table(parameters_headers, parameters_list)
if len(parameters) == 0:
parameters_table = "$$\\varnothing$$"
# Generate the code for the equations
psp, variables, pre_desc, post_desc = LatexParser._process_synapse_equations(synapse)
eqs = _process_variables(variables, neuron = False)
# PSP
if synapse.type == "rate":
psp = """
**Weighted sum:**
$$%(transmission)s$$
""" % {'transmission': psp}
elif synapse.type == "spike" and psp != "":
psp = """
**Continuous transmission:**
$$%(transmission)s$$
""" % {'transmission': psp}
else:
psp = ""
# Pre- and post-events
if synapse.type == "spike":
if len(pre_desc) > 0:
eqs += """
**Pre-synaptic event at $t_\\text{pre} + d$:**
"""
for pre in pre_desc:
eqs += "$$"+pre+"$$\n"
if len(post_desc) > 0:
eqs += """
**Post-synaptic event at $t_\\text{post}$:**
"""
for post in post_desc:
eqs += "$$"+post+"$$\n"
# Finalize the template
txt += synapse_tpl % { 'name': synapse_name,
'description': description,
'psp': psp,
'parameters': parameters_table,
'eqs': eqs}
return txt