Merge pull request #59 from NeuroML/experimental

Adding option to use string for percentage of inputs, e.g. containing…
NeuroML · Sep 11, 2023 · 5c9eb7c · 5c9eb7c
2 parents 77cd6f4 + 277200c
commit 5c9eb7c
Show file tree

Hide file tree

Showing 20 changed files with 13,918 additions and 13,909 deletions.
diff --git a/docs/NeuroMLlite_specification.json b/docs/NeuroMLlite_specification.json
@@ -446,7 +446,7 @@
                     "description": "Specific ids of _Cell_s to apply this input to (cannot be used with percentage"
                 },
                 "percentage": {
-                    "type": "float",
+                    "type": "Union[EvaluableExpression, List, Dict, ndarray, int, float, str]",
                     "description": "Percentage of Cells to apply input to"
                 },
                 "number_per_cell": {

diff --git a/docs/NeuroMLlite_specification.yaml b/docs/NeuroMLlite_specification.yaml
@@ -340,7 +340,8 @@ specification:
                 description: Specific ids of _Cell_s to apply this input to (cannot
                     be used with percentage
             percentage:
-                type: float
+                type: Union[EvaluableExpression, List, Dict, ndarray, int, float,
+                    str]
                 description: Percentage of Cells to apply input to
             number_per_cell:
                 type: Union[EvaluableExpression, List, Dict, ndarray, int, float,

diff --git a/docs/README.md b/docs/README.md
@@ -755,7 +755,7 @@ An Input definition.
 
   <tr>
     <td><b>percentage</b></td>
-    <td>float</td>
+    <td>Union[EvaluableExpression, List, Dict, ndarray, int, float, str]</td>
     <td><i>Percentage of Cells to apply input to</i></td>
  </tr>
 

diff --git a/examples/Example11_Synapses.json b/examples/Example11_Synapses.json
@@ -87,7 +87,7 @@
             "stim": {
                 "input_source": "i_clamp",
                 "population": "pop0",
-                "percentage": 100.0
+                "percentage": 100
             }
         }
     }

diff --git a/examples/Example12_MultiComp.json b/examples/Example12_MultiComp.json
@@ -113,7 +113,7 @@
             "stim": {
                 "input_source": "poissonFiringSyn",
                 "population": "pop_pyr",
-                "percentage": 100.0,
+                "percentage": 100,
                 "weight": "weightInput"
             }
         },

diff --git a/examples/Example2_TestNetwork.json b/examples/Example2_TestNetwork.json
@@ -71,7 +71,7 @@
             "stim_pop0": {
                 "input_source": "poissonFiringSyn",
                 "population": "pop0",
-                "percentage": 80.0
+                "percentage": 80
             }
         }
     }

diff --git a/examples/Example3_Network.json b/examples/Example3_Network.json
@@ -71,7 +71,7 @@
             "stim_pop0": {
                 "input_source": "poissonFiringSyn",
                 "population": "pop0",
-                "percentage": 80.0
+                "percentage": 80
             }
         }
     }

diff --git a/examples/Example4_PyNN.json b/examples/Example4_PyNN.json
@@ -120,7 +120,7 @@
             "stim": {
                 "input_source": "i_clamp",
                 "population": "pop0",
-                "percentage": 50.0
+                "percentage": 50
             }
         }
     }

diff --git a/examples/Example4_PyNN.net.nml b/examples/Example4_PyNN.net.nml
@@ -5,10 +5,10 @@
     NeuroMLlite parameters: 
         input_amp = 0.99</notes>
     <pulseGenerator id="i_clamp" delay="200.0ms" duration="600.0ms" amplitude="0.99nA"/>
-    <IF_cond_alpha id="testcell" cm="1." i_offset="0.1" tau_syn_E="0.3" tau_syn_I="0.5" v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50." e_rev_E="0." e_rev_I="-70."/>
-    <IF_cond_alpha id="testcell2" cm="1." i_offset="-0.1" tau_syn_E="2." tau_syn_I="10." v_init="-65." tau_m="20." tau_refrac="5." v_reset="-65." v_rest="-65." v_thresh="-50." e_rev_E="-10." e_rev_I="-80."/>
-    <alphaCondSynapse id="ampaSyn" tau_syn="2." e_rev="-10."/>
-    <alphaCondSynapse id="gabaSyn" tau_syn="10." e_rev="-80."/>
+    <IF_cond_alpha id="testcell" cm="1.0" i_offset="0.1" tau_syn_E="0.3" tau_syn_I="0.5" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="0.0" e_rev_I="-70.0"/>
+    <IF_cond_alpha id="testcell2" cm="1.0" i_offset="-0.1" tau_syn_E="2.0" tau_syn_I="10.0" v_init="-65.0" tau_m="20.0" tau_refrac="5.0" v_reset="-65.0" v_rest="-65.0" v_thresh="-50.0" e_rev_E="-10.0" e_rev_I="-80.0"/>
+    <alphaCondSynapse id="ampaSyn" tau_syn="2.0" e_rev="-10.0"/>
+    <alphaCondSynapse id="gabaSyn" tau_syn="10.0" e_rev="-80.0"/>
     <network id="Example4_PyNN">
         <notes>Example 4: a network with PyNN cells &amp; inputs</notes>
         <property tag="recommended_dt_ms" value="0.01"/>

diff --git a/examples/Example4_PyNN.yaml b/examples/Example4_PyNN.yaml
@@ -88,4 +88,4 @@ Example4_PyNN:
         stim:
             input_source: i_clamp
             population: pop0
-            percentage: 50.0
+            percentage: 50
diff --git a/examples/Example6_PyNN.net.nml b/examples/Example6_PyNN.net.nml
diff --git a/examples/Example6_PyNN_noinputs.net.nml b/examples/Example6_PyNN_noinputs.net.nml
diff --git a/examples/Example7_Brunel2000.net.nml b/examples/Example7_Brunel2000.net.nml
@@ -14,7 +14,7 @@
         tauRef = 2.0
         tauSyn = 0.1
         theta = 20.0</notes>
-    <IF_curr_alpha id="ifcell" cm="0.001" i_offset="0." tau_syn_E="0.1" tau_syn_I="0.1" v_init="0." tau_m="20." tau_refrac="2." v_reset="0." v_rest="0." v_thresh="20."/>
+    <IF_curr_alpha id="ifcell" cm="0.001" i_offset="0.0" tau_syn_E="0.1" tau_syn_I="0.1" v_init="0.0" tau_m="20.0" tau_refrac="2.0" v_reset="0.0" v_rest="0.0" v_thresh="20.0"/>
     <alphaCurrSynapse id="ampa" tau_syn="0.1"/>
     <alphaCurrSynapse id="gaba" tau_syn="0.1"/>
     <SpikeSourcePoisson id="poisson_input" start="0.0ms" duration="1000000000.0ms" rate="10000.0Hz"/>

diff --git a/examples/Example8_Extension.json b/examples/Example8_Extension.json
@@ -57,7 +57,7 @@
             "stim": {
                 "input_source": "poissonFiringSyn",
                 "population": "Epop",
-                "percentage": 50.0,
+                "percentage": 50,
                 "weight": "weightInput"
             }
         },

diff --git a/examples/LEMS_SimExample3.xml b/examples/LEMS_SimExample3.xml
@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.0.8 (libNeuroML v0.5.3)
+        This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
 
      -->
 

diff --git a/examples/LEMS_SimExample4.xml b/examples/LEMS_SimExample4.xml
@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.0.8 (libNeuroML v0.5.3)
+        This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
 
      -->
 

diff --git a/examples/spikeratetest/Spikers.json b/examples/spikeratetest/Spikers.json
@@ -85,18 +85,18 @@
             "stim0": {
                 "input_source": "poissonFiringSyn",
                 "population": "pop0",
-                "percentage": 50.0,
+                "percentage": 50,
                 "weight": "weightInput"
             },
             "stim1": {
                 "input_source": "iclamp1",
                 "population": "pop1",
-                "percentage": 100.0
+                "percentage": 100
             },
             "stim2": {
                 "input_source": "iclamp1",
                 "population": "pop2",
-                "percentage": 50.0
+                "percentage": 50
             }
         }
     }

diff --git a/neuromllite/NetworkGenerator.py b/neuromllite/NetworkGenerator.py
@@ -410,7 +410,7 @@ def generate_network(
                         if input.weight
                         else 1
                     )
-                    if flip * 100.0 < input.percentage:
+                    if flip * 100.0 < evaluate(input.percentage, nl_model.parameters, rng):
                         if input.number_per_cell and input.segment_ids:
                             raise Exception(
                                 "On input: %s, only one of number_per_cell or segment_ids is allowed"

diff --git a/neuromllite/__init__.py b/neuromllite/__init__.py
@@ -362,8 +362,8 @@ class Input(NMLBase):
     cell_ids: ValueExprType = field(
         default="", validator=optional(instance_of(value_expr_types))
     )
-    percentage: float = field(
-        default=None, validator=optional(instance_of(float)), converter=convert2float
+    percentage: ValueExprType = field(
+        default=None, validator=optional(instance_of(value_expr_types))
     )
     number_per_cell: ValueExprType = field(
         default="", validator=optional(instance_of(value_expr_types))

diff --git a/neuromllite/utils.py b/neuromllite/utils.py
@@ -80,6 +80,14 @@ def load_network_yaml(filename):
 
     return net
 
+def load_simulation(filename):
+    """
+    Load a NeuroMLlite simulation JSON/YAML file
+    """
+    if filename.endswith(".yaml") or filename.endswith(".yml"):
+        return load_simulation_yaml(filename)
+    else:
+        return load_simulation_json(filename)
 
 def load_simulation_json(filename: str) -> Optional[dict]:
     """
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,7 +2,7 @@ @@
         <!--
-            This LEMS file has been automatically generated using PyNeuroML v1.0.8 (libNeuroML v0.5.3)
+            This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
          -->
@@ Expand Down @@