[WIP] add a NetPyNE wrapper

hnn_core/netpyne_model.py

@@ -0,0 +1,272 @@
+import itertools as it
+from copy import deepcopy
+from collections import OrderedDict
+
+import numpy as np
+import warnings
+
+# from .drives import _drive_cell_event_times
+# from .drives import _get_target_properties, _add_drives_from_params
+# from .drives import _check_drive_parameter_values, _check_poisson_rates
+# from .cells_default import pyramidal, basket
+# from .params import _long_name, _short_name
+# from .viz import plot_cells
+# from .externals.mne import _validate_type, _check_option
+# from .extracellular import ExtracellularArray
+# from .check import _check_gids, _gid_to_type, _string_input_to_list
+
+
+from netpyne import specs, sim
+from neuron import h
+
+from netpyne.cell.inputs import createEvokedPattern
+
+
+class NetPyne_Model(object):
+    """The NetPyne_Model class.
+
+    Parameters
+    ----------
+    params : dict
+        The parameters to use for constructing the network.
+    add_drives_from_params : bool
+        If True, add drives as defined in the params-dict. NB this is mainly
+        for backward-compatibility with HNN GUI, and will be deprecated in a
+        future release. Default: False
+    legacy_mode : bool
+        Set to True by default to enable matching HNN GUI output when drives
+        are added suitably. Will be deprecated in a future release.
+
+    Attributes
+    ----------
+    cell_types : dict
+        Dictionary containing names of real cell types in the network
+        (e.g. 'L2_basket') as keys and corresponding Cell instances as values.
+        The Cell instance associated with a given key is used as a template
+        for the other cells of its type in the population.
+    gid_ranges : dict
+        A dictionary of unique identifiers of each real and artificial cell
+        in the network. Every cell type is represented by a key read from
+        cell_types, followed by keys read from external_drives. The value
+        of each key is a range of ints, one for each cell in given category.
+        Examples: 'L2_basket': range(0, 270), 'evdist1': range(272, 542), etc
+    pos_dict : dict
+        Dictionary containing the coordinate positions of all cells.
+        Keys are 'L2_pyramidal', 'L5_pyramidal', 'L2_basket', 'L5_basket',
+        or any external drive name
+    cell_response : CellResponse
+        An instance of the CellResponse object.
+    external_drives : dict (keys: drive names) of dict (keys: parameters)
+        The external driving inputs to the network. Drives are added by
+        defining their spike-time dynamics, and their connectivity to the real
+        cells of the network. Event times are instantiated before simulation,
+        and are stored under the ``'events'``-key (list of list; first
+        index for trials, second for event time lists for each drive cell).
+    external_biases : dict of dict (bias parameters for each cell type)
+        The parameters of bias inputs to cell somata, e.g., tonic current clamp
+    connectivity : list of dict
+        List of dictionaries specifying each cell-cell and drive-cell
+        connection
+    rec_arrays : dict
+        Stores electrode position information and voltages recorded by them
+        for extracellular potential measurements. Multiple electrode arrays
+        may be defined as unique keys. The values of the dictionary are
+        instances of :class:`hnn_core.extracellular.ExtracellularArray`.
+    threshold : float
+        Firing threshold of all cells.
+    delay : float
+        Synaptic delay in ms.
+
+    Notes
+    -----
+    ``net = jones_2009_model(params)`` is the reccomended path for creating a
+    network. Instantiating the network as ``net = Network(params)`` will
+    produce a network with no cell-to-cell connections. As such,
+    connectivity information contained in ``params`` will be ignored.
+    """
+
+    def __init__(self, params, add_drives_from_params=False,
+                 legacy_mode=False):
+        # Network parameters
+        netParams = specs.NetParams()  # object of class NetParams to store the network parameters
+
+        self.netParams = netParams
+
+         ## Cell parameters/rules
+        PYRcell = {'secs': {}}
+        PYRcell['secs']['soma'] = {'geom': {}, 'mechs': {}}  # soma params dict
+        PYRcell['secs']['soma']['geom'] = {'diam': '19 + uniform(-0.5, 0.5)', 'L': 18.8, 'Ra': 123.0}  # soma geometry
+        PYRcell['secs']['soma']['mechs']['hh'] = {'gnabar': '0.12 + 0.001*ynorm', 'gkbar': 0.036, 'gl': 0.003, 'el': -70}  # soma hh mechanism
+        self.netParams.cellParams['PYR'] = PYRcell
+
+        ## Population parameters
+        self.netParams.popParams['S'] = {'cellType': 'PYR', 'numCells': 20}
+        self.netParams.popParams['M'] = {'cellType': 'PYR', 'numCells': 20}
+
+        ## Synaptic mechanism parameters
+        self.netParams.synMechParams['exc'] = {'mod': 'Exp2Syn', 'tau1': 0.1, 'tau2': 5.0, 'e': 0}  # excitatory synaptic mechanism
+
+        ## Cell connectivity rules
+        self.netParams.connParams['S->M'] = {    #  S -> M label
+            'preConds': {'pop': 'S'},       # conditions of presyn cells
+            'postConds': {'pop': 'M'},      # conditions of postsyn cells
+            'probability': 0.5,
+            'weight': 0.01,                 # synaptic weight
+            'delay': 5, 
+            'synMech': 'exc'}               # synaptic mechanism
+
+
+
+    # def add_evoked_drive(self):
+
+    def add_evoked_drive(self, mu, sigma, numspikes, location,
+                         n_drive_cells, synaptic_delays=0.1,
+                         probability=1.0, event_seed=2):
+
+    # def add_evoked_drive(self, name, *, mu, sigma, numspikes, location,
+    #                      n_drive_cells='n_cells', cell_specific=True,
+    #                      weights_ampa=None, weights_nmda=None,
+    #                      space_constant=3., synaptic_delays=0.1,
+    #                      probability=1.0, event_seed=2, conn_seed=3):
+
+        """Add an 'evoked' external drive to the network
+
+        # create drive cells and connect them to the real cells defined in the init function
+
+        Parameters
+        ----------
+        name : str
+            Unique name for the drive
+        mu : float
+            Mean of Gaussian event time distribution
+        sigma : float
+            Standard deviation of event time distribution
+        numspikes : int
+            Number of spikes at each target cell
+        location : str
+            Target location of synapses. Must be an element of
+            `Cell.sect_loc` such as 'proximal' or 'distal', which defines a
+            group of sections, or an existing section such as 'soma' or
+            'apical_tuft' (defined in `Cell.sections` for all targeted cells).
+            The parameter `legacy_mode` of the `Network` must be set to `False`
+            to target specific sections.
+        n_drive_cells : int | 'n_cells'
+            The number of drive cells that each contribute an independently
+            sampled synaptic spike to the network according to the Gaussian
+            time distribution (mu, sigma). If n_drive_cells='n_cells'
+            (default) and cell_specific=True, a drive cell gets assigned to
+            each available simulated cell in the network with 1-to-1
+            connectivity. Otherwise, drive cells are assigned with
+            all-to-all connectivity. If you wish to synchronize the timing of
+            this evoked drive across the network in a given trial with one
+            spike, set n_drive_cells=1 and cell_specific=False.
+        cell_specific : bool
+            Whether each artifical drive cell has 1-to-1 (True, default) or
+            all-to-all (False) connection parameters. Note that 1-to-1
+            connectivity requires that n_drive_cells='n_cells', where 'n_cells'
+            denotes the number of all available cells that this drive can
+            target in the network.
+        weights_ampa : dict or None
+            Synaptic weights (in uS) of AMPA receptors on each targeted cell
+            type (dict keys). Cell types omitted from the dict are set to zero.
+        weights_nmda : dict or None
+            Synaptic weights (in uS) of NMDA receptors on each targeted cell
+            type (dict keys). Cell types omitted from the dict are set to zero.
+        synaptic_delays : dict or float
+            Synaptic delay (in ms) at the column origin, dispersed laterally as
+            a function of the space_constant. If float, applies to all target
+            cell types. Use dict to create delay->cell mapping.
+        space_constant : float
+            Describes lateral dispersion (from the column origin) of synaptic
+            weights and delays within the simulated column. The constant is
+            measured in the units of ``inplane_distance`` of
+            :class:`~hnn_core.Network`. For example, for ``space_constant=3``,
+            the weights are modulated by the factor
+            ``exp(-(x / (3 * inplane_distance)) ** 2)``, where x is the
+            physical distance (in um) between the connected cells in the xy
+            plane (delays are modulated by the inverse of this factor).
+        probability : dict or float (default: 1.0)
+            Probability of connection between any src-target pair.
+            Use dict to create probability->cell mapping. If float, applies to
+            all target cell types
+        event_seed : int
+            Optional initial seed for random number generator (default: 2).
+            Used to generate event times for drive cells.
+            Not fixed across trials (see Notes)
+        conn_seed : int
+            Optional initial seed for random number generator (default: 3).
+            Used to randomly remove connections when probablity < 1.0.
+            Fixed across trials (see Notes)
+
+        Notes
+        -----
+        Random seeding behavior across trials is different for event_seed
+        and conn_seed (n_trials > 1 in simulate_dipole(..., n_trials):
+
+        - event_seed
+            Across trials, the random seed is incremented leading such that
+            the exact spike times are different
+        - conn_seed
+            The random seed does not change across trials. This means for
+            probability < 1.0, the random subset of gids targeted is the same.
+        """
+
+
+        # Stimulation parameters
+        self.netParams.stimSourceParams['bkg'] = {'type': 'NetStim', 'rate': 10, 'noise': 0.5}
+        self.netParams.stimTargetParams['bkg->PYR'] = {'source': 'bkg', 'loc':location, 'conds': {'cellType': 'PYR'}, 'weight': 0.01, 'delay': synaptic_delays, 'synMech': 'exc'}
+
+
+        params = {'start':mu, 'startStd':sigma, 'numspikes':numspikes}
+        spkTimes = createEvokedPattern(params, rand=h.Random())
+
+        ## Population parameters
+        self.netParams.popParams['artif1'] = {'cellModel': 'NetStim', 'cellType': 'bkg', 'numCells': n_drive_cells, 'start':spkTimes[0], 'number':numspikes, 'seed':event_seed, 'spkTimes': spkTimes} 
+        self.netParams.popParams['artif2'] = {'cellModel': 'NetStim', 'cellType': 'bkg', 'numCells': n_drive_cells, 'start':spkTimes[0], 'number':numspikes, 'seed':event_seed, 'spkTimes': spkTimes}  # ??? VecStim with spike times
+
+
+        ## Cell connectivity rules
+        self.netParams.connParams['artif1->artif2'] = {    #  artif1 -> artif2 label
+            'preConds': {'pop': 'artif1'},       # conditions of presyn cells
+            'postConds': {'pop': 'artif2'},      # conditions of postsyn cells
+            'probability': probability,
+            'weight': 0.01,                 # synaptic weight
+            'delay': synaptic_delays, 
+            'loc': location, 
+            'synMech': 'exc'}               # synaptic mechanism
+
+
+
+def netpyne_model(params):
+	net = NetPyne_Model(params)
+	return net
+
+
+def simulate_dipole_netpyne(net,  dt=0.025, tstop=170):
+	# code to simulate netpyne model
+
+  # Simulation options
+  simConfig = specs.SimConfig()       # object of class SimConfig to store simulation configuration
+
+  simConfig.duration = tstop          # Duration of the simulation, in ms
+  simConfig.dt = dt                # Internal integration timestep to use
+  simConfig.verbose = False           # Show detailed messages
+  simConfig.recordTraces = {'V_soma':{'sec':'soma','loc':0.5,'var':'v'}}  # Dict with traces to record
+  simConfig.recordStep = 0.1          # Step size in ms to save data (eg. V traces, LFP, etc)
+  simConfig.filename = 'tutxxx'  # Set file output name
+  simConfig.savePickle = False        # Save params, network and sim output to pickle file
+  simConfig.saveJson = True
+
+  simConfig.analysis['plotRaster'] = {'saveFig': True}                  # Plot a raster
+  simConfig.analysis['plotTraces'] = {'include': [1,2,3,4,5], 'saveFig': True}  # Plot recorded traces for this list of cells
+  simConfig.analysis['plot2Dnet'] = {'saveFig': True}                   # plot 2D cell positions and connections
+
+  sim.createSimulateAnalyze(netParams = net.netParams, simConfig = simConfig)
+
+#   return ...
+
+
+
+
+
+