Merge pull request #486 from BlueBrain/jinja-template

update jinja template to have getCell function
BlueBrain · Feb 5, 2024 · 6fddc82 · 6fddc82
2 parents e05921d + e9f01c7
commit 6fddc82
Show file tree

Hide file tree

Showing 5 changed files with 25 additions and 0 deletions.
diff --git a/bluepyopt/ephys/templates/cell_template.jinja2 b/bluepyopt/ephys/templates/cell_template.jinja2
@@ -42,6 +42,10 @@ 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()
@@ -120,6 +124,7 @@ 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) {
+    // 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/examples/stochkv/stochkv3cell.hoc b/examples/stochkv/stochkv3cell.hoc
@@ -27,6 +27,10 @@ begintemplate stochkv3_cell
   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()
@@ -98,6 +102,7 @@ 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) {
+    // 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/examples/stochkv/stochkv3cell_det.hoc b/examples/stochkv/stochkv3cell_det.hoc
@@ -27,6 +27,10 @@ begintemplate stochkv3_cell
   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()
@@ -98,6 +102,7 @@ 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) {
+    // 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/examples/stochkv/stochkvcell.hoc b/examples/stochkv/stochkvcell.hoc
@@ -27,6 +27,10 @@ begintemplate stochkv_cell
   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()
@@ -98,6 +102,7 @@ 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) {
+    // 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/examples/stochkv/stochkvcell_det.hoc b/examples/stochkv/stochkvcell_det.hoc
@@ -27,6 +27,10 @@ begintemplate stochkv_cell
   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()
@@ -98,6 +102,7 @@ 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) {
+    // 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)
   }