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
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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)
  }