Made updates based on running examples

suny-downstate-medical-center · Oct 29, 2021 · e7a1a3f · e7a1a3f
1 parent 1dd834f
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diff --git a/netpyne/sim/setup.py b/netpyne/sim/setup.py
@@ -18,7 +18,7 @@
 from neuron import h # Import NEURON
 from .. import specs
 from ..specs import Dict, ODict
-from . import utils
+from . import utils, validator
 try:
     from datetime import datetime
 except:
@@ -51,7 +51,6 @@ def initialize(netParams = None, simConfig = None, net = None):
 
     """
 
-
     from .. import sim
 
     if netParams is None: netParams = {} # If not specified, initialize as empty dict
@@ -60,6 +59,11 @@ def initialize(netParams = None, simConfig = None, net = None):
         print('Error: seems like the sim.initialize() arguments are in the wrong order, try initialize(netParams, simConfig)')
         sys.exit()
 
+    if validator.validate_netparams(netParams):
+        print('Good to go')
+    else:
+        print('Bad parameters')
+
     # for testing validation
     # if simConfig.exitOnError:
     #sys.exit()

diff --git a/netpyne/sim/validator.py b/netpyne/sim/validator.py
@@ -0,0 +1,166 @@
+from schema import Schema, Optional, And, Or, Use
+from collections import ChainMap
+
+cell_spec = {
+    str: {
+        'secs': {
+#            Optional(And(str, Use(str.lower), lambda s: s in ['soma', 'dend'])): {
+            Optional(str): {
+                Optional('geom'): {
+                    Optional('L'): Or(int, float),
+                    Optional('Ra'): Or(int, float),
+                    Optional('diam'): Or(int, float),
+                    Optional('cm'): Or(int, float),
+                    Optional('pt3d'): And([(float, float, float, float)],
+                                          lambda t: len(list(filter(lambda x: len(x) != 4, t))) == 0),
+                    Optional('nseg'): Or(int, float)
+                },
+                Optional('mechs'): {
+                    And(str, Use(str.lower), lambda s: s in ['hh', 'pas']): {
+                        Optional('el'): int,
+                        Optional('gkbar'): float,
+                        Optional('gl'): float,
+                        Optional('gnabar'): float,
+                        Optional('g'): float,
+                        Optional('e'): Or(int, float),
+                    },
+                    Optional('Nafbwb'): {},
+                    Optional('Kdrbwb'): {},
+                    Optional('Caolmw'): {},
+                    Optional('Iholmw'): {},
+                    Optional('ICaolmw'): {},
+                    Optional('KCaolmw'): {},
+                    Optional('nacurrent'): {
+                        Optional('ki'): Or(int,float)
+                    },
+                    Optional('kacurrent'): {},
+                    Optional('kdrcurrent'): {},
+                    Optional('hcurrent'): {}
+                },
+                Optional('topol'): {
+                    Optional('parentSec'): And(str, Use(str.lower), lambda s: s in ['soma', 'dend']),
+                    Optional('childX'): Or(int, float),
+                    Optional('parentX'): Or(int, float)
+                },
+                Optional('pointps'): {
+                    str: {
+                        'mod': str,
+                        'C': Or(int, float),
+                        'k': Or(int, float),
+                        'vr': Or(int, float),
+                        'vt': Or(int, float),
+                        'vpeak': Or(int, float),
+                        'a': Or(int, float),
+                        'b': Or(int, float),
+                        'c': Or(int, float),
+                        'd': Or(int, float),
+                        'celltype': int
+                    }
+                },
+                Optional('vinit'): Or(int, float)
+            }
+        }
+    }
+}
+
+population_spec = {
+    str: {
+        'cellType': str,
+        'numCells': int,
+        Optional('yRange'): [int],
+        Optional('ynormRange'): [float],
+        Optional('cellModel'): str
+    }
+}
+
+
+synaptic_spec = {
+    str: {
+        'mod': And(str, Use(str.lower), lambda s: s in ['exp2syn']),
+        'tau1': Or(int, float),
+        'tau2': Or(int, float),
+        'e': Or(int, float)
+    }
+}
+
+
+stimulation_source_spec = {
+    str: {
+        Optional('type'): And(str, Use(str.lower), lambda s: s in ['iclamp', 'vclamp', 'alphasynapse', 'netstim']),
+        Optional('rate'): int,
+        Optional('noise'): float,
+        Optional('del'): int,
+        Optional('dur'): Or(int, [int]),
+        Optional('amp'): Or(str, [int]),
+        Optional('gain'): float,
+        Optional('tau1'): Or(int, float),
+        Optional('tau2'): Or(int, float),
+        Optional('rstim'): Or(int, float),
+        Optional('e'): Or(int, float),
+        Optional('gmax'): str,
+        Optional('onset'): str,
+        Optional('tau'): Or(int, float),
+        Optional('interval'): str,
+        Optional('start'): Or(int, float)
+    }
+}
+
+
+stimulation_target_spec = {
+    str: {
+        Optional('source'): str,
+        Optional('conds'): {
+            Optional('cellType'): Or(str, [str]),
+            Optional('cellList'): [Or(int, float)],
+            Optional('pop'): str,
+            Optional('ynorm'): [Or(int, float)]
+        },
+        Optional('weight'): Or(float, str),  # The string is for capturing functions. May want to validate it's valid python
+        Optional('delay'): Or(int, str),  # The string is for capturing functions. May want to validate it's valid python
+        Optional('synMech'): str,
+        Optional('loc'): float,
+        Optional('sec'): str
+    }
+}
+
+
+connection_spec = {
+    str: {
+        Optional('preConds'): {
+            Optional('pop'): Or(str, [str]),
+            Optional('y'): [Or(int, float)],
+            Optional('cellType'): str
+        },
+        Optional('postConds'): {
+            Optional('pop'): Or(str, [str]),
+            Optional('y'): [Or(int, float)],
+            Optional('cellType'): str
+        },
+        Optional(And(str, Use(str.lower), lambda s: s in ['probability', 'convergence', 'divergence'])): Or(float, str),
+        Optional('weight'): Or(float, str),  # The string is for capturing functions. May want to validate it's valid python
+        Optional('delay'): Or(int, str),  # The string is for capturing functions. May want to validate it's valid python
+        Optional('synMech'): str,
+        Optional('loc'): float,
+        Optional('sec'): And(str, Use(str.lower), lambda s: s in ['dend'])
+    }
+}
+
+
+cell_schema = Schema(cell_spec)
+population_schema = Schema(population_spec)
+synaptic_schema = Schema(synaptic_spec)
+stimulation_source_schema = Schema(stimulation_source_spec)
+stimulation_target_schema = Schema(stimulation_target_spec)
+connection_schema = Schema(connection_spec)
+
+# Attempt to merge schemas -- This doesn't work yet so we'll check the pieces one by one
+net_param_schema = Schema(dict(ChainMap(*[cell_spec, population_spec, synaptic_spec, stimulation_source_spec,
+                                          stimulation_target_spec, connection_spec])))
+
+
+def validate_netparams(net_params):
+    return cell_schema.validate(net_params.cellParams) and \
+    population_schema.validate(net_params.popParams) and \
+    synaptic_schema.validate(net_params.synMechParams) and \
+    stimulation_source_schema.validate(net_params.stimSourceParams) and \
+    stimulation_target_schema.validate(net_params.stimTargetParams)
diff --git a/requirements.txt b/requirements.txt
@@ -8,3 +8,4 @@ bokeh
 pyneuroml
 neuron
 pytest
+schema
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,3 +8,4 @@ bokeh @@
     pyneuroml
     neuron
     pytest
+    schema