Updated virtual neuron code

Hjorthmedh · Nov 24, 2023 · 788e95a · 788e95a
1 parent f15ac97
commit 788e95a
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Showing 5 changed files with 8,025 additions and 402 deletions.
diff --git a/examples/notebooks/lateral_inhitibion/input-virtual.json b/examples/notebooks/lateral_inhitibion/input-virtual.json
@@ -0,0 +1,68 @@
+{
+    "dSPN": {
+        "Ctx_1" : {
+            "generator" : "poisson",
+            "start" : [0.5, 3.5],
+            "end" : [1.5, 4.5],
+            "frequency" : [25, 25],
+            "conductance" : 0.5e-9,
+            "nInputs" : 50,
+            "populationUnitCorrelation" : [0.5, 0.5],
+            "populationUnitID" : 1,
+            "jitter" : 0.01,	    
+            "modFile": "tmGlut"
+        },
+
+	"Ctx_2" : {
+            "generator" : "poisson",
+            "start" : [2, 3.5],
+            "end" : [3, 4.5],
+            "frequency" : [5, 5],
+            "conductance" : 0.5e-9,
+            "nInputs" : 50,
+            "populationUnitCorrelation" : [0.5, 0.5],
+            "populationUnitID" : 2,
+            "jitter" : 0.01,	    
+            "modFile": "tmGlut"
+        },
+
+	"VirtualNeuron" : {
+            "spikeFile": "virtual_input_spikes.txt",
+            "rowMappingFile": "virtual_input_mapping.txt"
+	}		
+    },
+
+    "iSPN": {
+        "Ctx_1" : {
+            "generator" : "poisson",
+            "start" : [0.5, 3.5],
+            "end" : [1.5, 4.5],
+            "frequency" : [25, 25],
+            "conductance" : 0.5e-9,
+            "nInputs" : 50,
+            "populationUnitCorrelation" : [0.5, 0.5],
+            "populationUnitID" : 1,	    
+            "jitter" : 0.01,	    
+            "modFile": "tmGlut"
+        },
+
+        "Ctx_2" : {
+            "generator" : "poisson",
+            "start" : [2, 3.5],
+            "end" : [3, 4.5],
+            "frequency" : [5, 5],
+            "conductance" : 0.5e-9,
+            "nInputs" : 50,
+            "populationUnitCorrelation" : [0.5, 0.5],
+            "populationUnitID" : 2,	    
+            "jitter" : 0.01,	    
+            "modFile": "tmGlut"
+        },
+
+	"VirtualNeuron" : {
+            "spikeFile": "virtual_input_spikes.txt",
+            "rowMappingFile": "virtual_input_mapping.txt"
+	}
+    }
+
+}
diff --git a/examples/notebooks/lateral_inhitibion/lateral_inhibition_virtual.ipynb b/examples/notebooks/lateral_inhitibion/lateral_inhibition_virtual.ipynb
diff --git a/...lel/KTH_PDC/lateral_inhibition/one_population/Analyse One Population-voltage-GABA90.ipynb b/...lel/KTH_PDC/lateral_inhibition/one_population/Analyse One Population-voltage-GABA90.ipynb
diff --git a/snudda/plotting/plot_neuron_voltage.py b/snudda/plotting/plot_neuron_voltage.py
@@ -74,7 +74,12 @@ def plot_neuron_voltage(self, neuron_id, section_id=None, axis=None,
 
         time, volt, sec_id, sec_x = self.get_voltage_sec(neuron_id=neuron_id, section_id=section_id)
 
-        ax.plot(time, volt)
+        soma_dist = self.get_soma_dist(neuron_id=neuron_id, section_id=sec_id, section_x=sec_x)
+        label = [f"Neuron {neuron_id}, sec {sid}:{sx}, dist {sd*1e6:.1f} um" for (sid, sx, sd) in zip(sec_id, sec_x, soma_dist)]
+
+        ax.plot(time, volt, label=label)
+
+        plt.legend()
 
         if fig_name:
             self.create_fig_dir(fig_name)
@@ -86,6 +91,13 @@ def plot_neuron_voltage(self, neuron_id, section_id=None, axis=None,
 
         return ax
 
+    def list_all_section_dist(self, neuron_id):
+
+        morphology = self.load_morphology(neuron_id=neuron_id)
+
+        for section in morphology.morphology_data["neuron"].sections[3].values():
+            print(f"Section {section.section_id}, center dist {section.soma_distance_at(0.5)*1e6:.0f} um, length {section.section_length()*1e6:.0f} um")
+
     def create_fig_dir(self, fig_path):
 
         fig_dir = os.path.dirname(fig_path)
@@ -115,21 +127,8 @@ def plot_binned_neuron_voltage(self, neuron_id, time_bins, section_id=None, dist
         else:
             ax = axis
 
-        morphology = self.load_morphology(neuron_id=neuron_id)
-
         time, volt, sec_id, sec_x = self.get_voltage_sec(neuron_id=neuron_id, section_id=section_id)
-
-        soma_dist = np.zeros(sec_id.shape)
-
-        for idx, (s_id, s_x) in enumerate(zip(sec_id, sec_x)):
-
-            if s_id < 0:
-                sec_type = 1  # soma
-                s_id = 0
-            else:
-                sec_type = 3  # dend
-
-            soma_dist[idx] = morphology.morphology_data["neuron"].sections[sec_type][s_id].soma_distance_at(s_x)
+        soma_dist = self.get_soma_dist(neuron_id=neuron_id, section_id=sec_id, section_x=sec_x)
 
         # First bin is soma only, bins after are for dendrites (with binwidth dist_bin_size)
         bin_idx = np.floor(soma_dist / dist_bin_size).astype(int) + 1
@@ -191,6 +190,25 @@ def plot_binned_neuron_voltage(self, neuron_id, time_bins, section_id=None, dist
         return ax
 
 
+    def get_soma_dist(self, neuron_id, section_id, section_x):
+
+        morphology = self.load_morphology(neuron_id=neuron_id)
+
+        soma_dist = np.zeros(section_id.shape)
+
+        for idx, (sec_id, sec_x) in enumerate(zip(section_id, section_x)):
+
+            if sec_id < 0:
+                sec_type = 1  # soma
+                sec_id = 0
+            else:
+                sec_type = 3  # dend
+
+            soma_dist[idx] = morphology.morphology_data["neuron"].sections[sec_type][sec_id].soma_distance_at(sec_x)
+
+        return soma_dist
+
+
 def cli():
 
     import argparse

diff --git a/snudda/utils/ablate_network.py b/snudda/utils/ablate_network.py
@@ -80,7 +80,7 @@ def make_virtual(self, neuron_id):
         if type(neuron_id) == list:
             self.make_virtual_neuron_id += neuron_id
         elif isinstance(neuron_id, np.ndarray):
-            self.make_virtual_neuron_id += [x for x in np.ndarray]
+            self.make_virtual_neuron_id += [x for x in neuron_id]
         else:
             self.make_virtual_neuron_id.append(neuron_id)