From 41da32b38ecaf87ce95782d503498035ccbadd32 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?=
 <aurelien.jaquier@epfl.ch>
Date: Fri, 2 Feb 2024 16:48:43 +0100
Subject: [PATCH] update jinja templates

---
 .../templates/cell_template_neurodamus.jinja2 |  3 ++-
 .../cell_template_neurodamus_sbo.jinja2       | 24 ++++++++++++++-----
 .../templates/cell_template_neuron.jinja2     |  7 +++++-
 3 files changed, 26 insertions(+), 8 deletions(-)

diff --git a/bluepymm/templates/cell_template_neurodamus.jinja2 b/bluepymm/templates/cell_template_neurodamus.jinja2
index 5120b2ec..fa9532bc 100755
--- a/bluepymm/templates/cell_template_neurodamus.jinja2
+++ b/bluepymm/templates/cell_template_neurodamus.jinja2
@@ -184,7 +184,8 @@ proc distribute_distance(){local x localobj sl
   this.soma[0] distance(0, 0.5)
   sprint(distfunc, "%%s %s(%%f) = %s", mech, distfunc)
   forsec sl for(x, 0) {
-    sprint(stmp, distfunc, secname(), x, distance(x))
+    // use distance(x) twice for the step distribution case, e.g. for calcium hotspot
+    sprint(stmp, distfunc, secname(), x, distance(x), distance(x))
     execute(stmp)
   }
 }
diff --git a/bluepymm/templates/cell_template_neurodamus_sbo.jinja2 b/bluepymm/templates/cell_template_neurodamus_sbo.jinja2
index 8b57dfbf..fceb1024 100644
--- a/bluepymm/templates/cell_template_neurodamus_sbo.jinja2
+++ b/bluepymm/templates/cell_template_neurodamus_sbo.jinja2
@@ -138,16 +138,27 @@ func getThreshold() { return 0.0 }
 
 proc load_morphology(/* morphology_dir, morphology_name */) {localobj morph, import, sf, extension, commands, pyobj
   strdef morph_path
-  sprint(morph_path, "%s/%s", $s1, $s2)  sf = new StringFunctions()
-  extension = new String()  sscanf(morph_path, "%s", extension.s)
+  sprint(morph_path, "%s/%s", $s1, $s2)
+  sf = new StringFunctions()
+  extension = new String()
+  sscanf(morph_path, "%s", extension.s)
 
-  // TODO fix the `-3` here.
   sf.right(extension.s, sf.len(extension.s)-3)
   
-  if( strcmp(extension.s, ".asc") == 0 ) {
+  if( strcmp(extension.s, "asc") == 0 ) {
      morph = new Import3d_Neurolucida3()
-  } else if( strcmp(extension.s, ".swc" ) == 0) {
+     morph.quiet = 1
+     morph.input(morph_path)
+
+     import = new Import3d_GUI(morph, 0)
+     import.instantiate(this)
+  } else if( strcmp(extension.s, "swc" ) == 0) {
      morph = new Import3d_SWC_read()
+     morph.quiet = 1
+     morph.input(morph_path)
+
+     import = new Import3d_GUI(morph, 0)
+     import.instantiate(this)
   } else if( strcmp(extension.s, ".h5") == 0 ) {
     if(nrnpython ("from morphio_wrapper import MorphIOWrapper") == 1) {
         pyobj = new PythonObject()
@@ -181,7 +192,8 @@ proc distribute_distance(){local x localobj sl
   this.soma[0] distance(0, 0.5)
   sprint(distfunc, "%%s %s(%%f) = %s", mech, distfunc)
   forsec sl for(x, 0) {
-    sprint(stmp, distfunc, secname(), x, distance(x))
+    // use distance(x) twice for the step distribution case, e.g. for calcium hotspot
+    sprint(stmp, distfunc, secname(), x, distance(x), distance(x))
     execute(stmp)
   }
 }
diff --git a/bluepymm/templates/cell_template_neuron.jinja2 b/bluepymm/templates/cell_template_neuron.jinja2
index 85a1974e..5102f379 100755
--- a/bluepymm/templates/cell_template_neuron.jinja2
+++ b/bluepymm/templates/cell_template_neuron.jinja2
@@ -41,6 +41,10 @@ begintemplate {{template_name}}
   public all, somatic, apical, axonal, basal, myelinated, APC
   objref all, somatic, apical, axonal, basal, myelinated, APC
 
+obfunc getCell(){
+        return this
+}
+
 proc init(/* args: morphology_dir, morphology_name */) {
   all = new SectionList()
   apical = new SectionList()
@@ -112,7 +116,8 @@ proc distribute_distance(){local x localobj sl
   this.soma[0] distance(0, 0.5)
   sprint(distfunc, "%%s %s(%%f) = %s", mech, distfunc)
   forsec sl for(x, 0) {
-    sprint(stmp, distfunc, secname(), x, distance(x))
+    // use distance(x) twice for the step distribution case, e.g. for calcium hotspot
+    sprint(stmp, distfunc, secname(), x, distance(x), distance(x))
     execute(stmp)
   }
 }