Update units for NEURON

Hjorthmedh · Aug 21, 2024 · 36bf912 · 36bf912
1 parent 0b24fce
commit 36bf912
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Showing 2 changed files with 33 additions and 8 deletions.
diff --git a/examples/notebooks/neuromodulation/neuromodulation_bath.ipynb b/examples/notebooks/neuromodulation/neuromodulation_bath.ipynb
@@ -212,10 +212,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "id": "d84ee6f3-4193-4509-ad4a-0d93dff5e3d9",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Loading networks/neuromodulation_bath/simulation/output.hdf5\n"
+     ]
+    }
+   ],
    "source": [
     "from snudda.utils import SnuddaLoadSimulation\n",
     "\n",
@@ -232,7 +240,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "id": "bd0f4edf-a622-490b-b39f-18f516975737",
    "metadata": {},
    "outputs": [],
@@ -244,10 +252,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "id": "a63a7152-730e-4868-a81a-cc87fccaf9f4",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<iframe\n",
+       "    scrolling=\"no\"\n",
+       "    width=\"1020px\"\n",
+       "    height=\"820\"\n",
+       "    src=\"iframe_figures/figure_8.html\"\n",
+       "    frameborder=\"0\"\n",
+       "    allowfullscreen\n",
+       "></iframe>\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "import plotly.graph_objects as go\n",
     "import plotly.io as pio\n",

diff --git a/snudda/simulate/simulate.py b/snudda/simulate/simulate.py
@@ -368,7 +368,7 @@ def setup_parse_sim_info(self):
                 for species_name, bath_info in self.sim_info["bath_application"].items():
 
                     bath_time = np.array(bath_info["time"])
-                    bath_conc = np.array(bath_info["concentration"]) * 1e6  # convert from SI to micromolar
+                    bath_conc = np.array(bath_info["concentration"])
                     neuron_id = bath_info.get("neuron_id", None)
 
                     self.add_bath_application(species_name=species_name,
@@ -2020,8 +2020,8 @@ def add_bath_application(self, species_name, concentration, time, neuron_id=None
         if neuron_id is None:
             neuron_id = self.snudda_loader.get_neuron_id(include_virtual=False)
 
-        conc_vect = self.sim.neuron.h.Vector(concentration)
-        t_vect = self.sim.neuron.h.Vector(time)
+        conc_vect = self.sim.neuron.h.Vector(concentration * 1e6)  # SI to micromolar
+        t_vect = self.sim.neuron.h.Vector(time * 1e3)  # s -> ms
 
         if species_name is self.bath_application:
             raise KeyError(f"Bath application already applied for {species_name}")