Merge pull request #51 from sparsh-989/spatialneuron

Change for adaption of equations of spatial neuron except morphology

brian2tools/baseexport/collector.py

@@ -94,6 +94,96 @@ def collect_NeuronGroup(group, run_namespace):
 
     return neuron_dict
 
+def collect_SpatialNeuron(group, run_namespace):
+
+    """
+    Collect information from `brian2.spatialneuron.spatialneuron.SpatialNeuron`
+    and return them in a dictionary format
+
+    Parameters
+    ----------
+    group : brian2.spatialneuron.spatialneuron.SpatialNeuron
+    SpatialNeuron object
+
+    run_namespace : dict
+        Namespace dictionary
+
+    Returns
+    -------
+    neuron_dict : dict
+        Dictionary with extracted information
+    """
+
+
+    neuron_dict = {}
+
+    # identifiers belonging to the NeuronGroup
+    identifiers = set()
+
+    # get name
+    neuron_dict['name'] = group.name
+
+    # get size
+    neuron_dict['N'] = group._N
+
+    # get user defined stateupdation method
+    if isinstance(group.method_choice, str):
+        neuron_dict['user_method'] = group.method_choice
+    # if not specified by user
+    # TODO collect from run time
+    else:
+        neuron_dict['user_method'] = None
+
+    # get equations
+    neuron_dict['equations'] = collect_Equations(group.user_equations)
+    identifiers = identifiers | group.user_equations.identifiers
+
+    neuron_dict['morphology'] = {}
+    if group is not None and group.morphology is not None:
+        morphology = group.morphology
+        neuron_dict["morphology"]["total_compartments"] = group.N
+        area_variable = group.area.get_item(group)
+        if isinstance(area_variable, np.ndarray):
+            neuron_dict["morphology"]["area"] = np.sum(area_variable)
+        neuron_dict["morphology"]["total_sections"] = morphology.total_sections
+
+
+    # check spike event is defined
+    if group.events:
+        neuron_dict['events'], event_identifiers = collect_Events(group)
+        identifiers = identifiers | event_identifiers
+
+    # check any `run_regularly` / CodeRunner objects associated
+    for obj in group.contained_objects:
+        # Note: Thresholder, StateUpdater, Resetter are all derived from
+        # CodeRunner, so to identify `run_regularly` object we use type()
+        if type(obj) == CodeRunner:
+            if 'run_regularly' not in neuron_dict:
+                neuron_dict['run_regularly'] = []
+            neuron_dict['run_regularly'].append({
+                                            'name': obj.name,
+                                            'code': obj.abstract_code,
+                                            'dt': obj.clock.dt,
+                                            'when': obj.when,
+                                            'order': obj.order
+                                            })
+            identifiers = identifiers | get_identifiers(obj.abstract_code)
+
+        # check StateUpdater when/order and assign to group level
+        if isinstance(obj, StateUpdater):
+            neuron_dict['when'] = obj.when
+            neuron_dict['order'] = obj.order
+
+    # resolve group-specific identifiers
+    identifiers = group.resolve_all(identifiers, run_namespace)
+    # with the identifiers connected to group, prune away unwanted
+    identifiers = _prepare_identifiers(identifiers)
+    # check the dictionary is not empty
+    if identifiers:
+        neuron_dict['identifiers'] = identifiers
+
+    return neuron_dict
+
 
 def collect_Equations(equations):
     """

brian2tools/baseexport/device.py

@@ -1,6 +1,7 @@
 from brian2.core.variables import DynamicArrayVariable
 from brian2.devices.device import RuntimeDevice, Device, all_devices
 from brian2.groups import NeuronGroup
+from brian2.spatialneuron import SpatialNeuron
 from brian2.input import PoissonGroup, SpikeGeneratorGroup
 from brian2 import (get_local_namespace, StateMonitor, SpikeMonitor,
                     EventMonitor, PopulationRateMonitor, Synapses,
@@ -53,7 +54,7 @@ def __init__(self):
         self.build_on_run = True
         self.has_been_run = False
         self.build_options = None
-        self.supported_objs = (NeuronGroup, SpikeGeneratorGroup,
+        self.supported_objs = (NeuronGroup, SpatialNeuron, SpikeGeneratorGroup,
                                PoissonGroup, StateMonitor, SpikeMonitor,
                                EventMonitor, PopulationRateMonitor, Synapses,
                                PoissonInput)
@@ -139,6 +140,7 @@ def network_run(self, network, duration, namespace=None, level=0, **kwds):
 
         # dictionary to store objects and its collector functions
         collector_map={'neurongroup': {'f': collect_NeuronGroup, 'n': True},
+                       'spatialneuron': {'f': collect_SpatialNeuron, 'n': True},
                        'poissongroup': {'f': collect_PoissonGroup, 'n': True},
                        'spikegeneratorgroup': {'f': collect_SpikeGenerator,
                                                'n': True},

brian2tools/mdexport/expander.py

@@ -321,6 +321,11 @@ def create_md_string(self, net_dict, template_name):
                     "h": "Neuron population",
                     "order": 1,
                 },
+                "spatialneuron": {
+                        "hb": "SpatialNeuron",
+                        "h": "Neuron population",
+                        "order": 1
+                }, 
                 "poissongroup": {
                     "hb": "PoissonGroup",
                     "h": "Poisson spike source",

brian2tools/templates/SpatialNeuron-default.md

@@ -0,0 +1,43 @@
+## Network details
+ **Neuron population:**
+Group {{ (group['name']) }}, consisting of {{ (group['N']) }} neurons.
+{{ tab }}{{ ('Model dynamics:') }}
+{{ expander.expand_equations(group['equations']) }}
+# **Morphology:**
+
+{% if 'area' in group['morphology'] %}
+    Area: {{ group['morphology']['area'] }}
+{% endif %}
+
+{% if 'total_sections' in group['morphology'] %}
+    Total Sections: {{ group['morphology']['total_sections'] }}
+{% endif %}
+
+{% if 'total_compartments' in group['morphology'] %}
+    Total Compartments: {{ group['morphology']['total_compartments'] }}
+{% endif %}
+ {% if group['user_method'] %}
+    {{ tab }}The equations are integrated with the '{{ group['user_method'] }}' method.
+{% endif %}
+{% if 'events' in group %}
+    {{ tab }}{{ ('Events:') }}
+    {{ expander.expand_events(group['events']) }}
+{% endif %}
+{% if 'identifiers' in group %}
+    {{ tab }}{{ ('Constants:') }} {{ expander.expand_identifiers(group['identifiers']) }}
+{% endif %}
+{% if not expander.keep_initializer_order and 'initializer' in group and group['initializer']|length %}
+    {{ tab }}{{ ('Initial values:') }}
+    {% for initializer in group['initializer'] %}
+        {{ tab }}* {{ expander.expand_initializer(initializer) }}
+    {% endfor %}
+{% endif %}
+{% if 'run_regularly' in group %}
+    {{ tab }}{{ ('Run regularly') }}{{ expander.check_plural(group['run_regularly']) }}:
+    {% for run_reg in group['run_regularly'] %}
+        {{ expander.expand_runregularly(run_reg) }}
+    {% endfor %}
+{% endif %}
+
+
+

brian2tools/templates/SpatialNeuron-table.md

@@ -0,0 +1,8 @@
+|-------------------------------|------------------------------------------------|
+| **Neuron population**         | Group {{ (group['name']) }}, consisting of {{ (group['N']) }} neurons. |
+| **Model dynamics**            | {{ expander.expand_equations(group['equations']) }} |
+| **Integration method**        | {% if group['user_method'] %} The equations are integrated with the '{{ group['user_method'] }}' method. {% endif %} |
+| **Events** (if present)       | {% if 'events' in group %} {{ expander.expand_events(group['events']) }} {% endif %} |
+| **Constants** (if present)    | {% if 'identifiers' in group %} {{ expander.expand_identifiers(group['identifiers']) }} {% endif %} |
+| **Initial values** (if present)| {% if not expander.keep_initializer_order and 'initializer' in group and group['initializer']|length %} {% for initializer in group['initializer'] %} {{ initializer.variable }}: {{ initializer.value }}{% if initializer.unit %} [{{ initializer.unit }}]{% endif %} {% if not loop.last %}\n{% endif %}{% endfor %} {% endif %} |
+| **Run regularly** (if present)| {% if 'run_regularly' in group %} {% for run_reg in group['run_regularly'] %} {{ expander.expand_runregularly(run_reg) }} {% if not loop.last %}\n{% endif %}{% endfor %} {% endif %} |