pt3dstyle logical connection should be at center of soma section (instead of center of contour).

share/lib/hoc/import3d/import3d_gui.hoc

@@ -1041,7 +1041,7 @@ func set_nameindex() {local i, min  localobj sec
   * @param $2 (optional) If set to 1, will keep a public reference to a list of strings that were executed by this method (commands).
   */
 
-proc instantiate() {local i, j, min, haspy, ispycontext, keepCommands  localobj sec, xx, yy, zz, dd, pyobj, allpyobjs
+proc instantiate() {local i, j, min, haspy, ispycontext, keepCommands  localobj sec, psec, xx, yy, zz, dd, pyobj, allpyobjs
 	commands = new List()
 	chk_valid()
 	haspy = nrnpython("import neuron")
@@ -1077,6 +1077,7 @@ proc instantiate() {local i, j, min, haspy, ispycontext, keepCommands  localobj
 	// connect
 	for i = 0, swc.sections.count-1 {
 		sec = swc.sections.object(i)
+		psec = sec.parentsec
 		if (sec.is_subsidiary) { continue }
 		name(sec, tstr)
 		if (i == 0 && !ispycontext) {
@@ -1086,25 +1087,33 @@ proc instantiate() {local i, j, min, haspy, ispycontext, keepCommands  localobj
 				execute(tstr1, $o1)
 			}
 		}
-		if (sec.parentsec != nil) {
-			name(sec.parentsec, tstr1)
+		if (psec != nil) {
+			name(psec, tstr1)
 			if (!ispycontext) {
 			    sprint(tstr1, "%s connect %s(0), %g\n", tstr1, tstr, sec.parentx)
 			    commands.append(new String(tstr1))
 				execute(tstr1, $o1)
-		    } else {
-		        pyobj.neuron._connect_sections_in_obj($o1, tstr, 0, tstr1, sec.parentx)
-		    }
+			} else {
+		            pyobj.neuron._connect_sections_in_obj($o1, tstr, 0, tstr1, sec.parentx)
+			}
 		}
 		// 3-d point info
 		if (sec.first == 1) {
+                    // if psec is contour, update logical connection
+		    if (psec != nil) {
+		        if (psec.iscontour_) {
+		            for j = 0, 2 {
+			        sec.raw.x[j][0] = psec.processed_contour_center.x[j]
+		            }
+		        }
+		    }
 		    if (ispycontext) {
 		        pyobj.neuron._pt3dstyle_in_obj($o1, tstr, sec.raw.x[0][0], sec.raw.x[1][0], sec.raw.x[2][0])
 		    } else {
 			    sprint(tstr1, "%s { pt3dstyle(1, %.8g, %.8g, %.8g) }\n", tstr, sec.raw.x[0][0], sec.raw.x[1][0], sec.raw.x[2][0])
 			    commands.append(new String(tstr1))
 				execute(tstr1, $o1)
-            }
+                    }
 		}
 		j = sec.first
 		xx = sec.raw.getrow(0).c(j)
@@ -1199,12 +1208,13 @@ proc mksubset() {
 	execute(tstr1, $o1)
 }
 
-proc contour2centroid() {local i, j, imax, imin, ok  localobj mean, pts, d, max, min, tobj, rad, rad2, side2, pt, major, m, minor
+proc contour2centroid() {local i, j, imax, imin, ok  localobj sec, mean, pts, d, max, min, tobj, rad, rad2, side2, pt, major, m, minor
 	if (object_id($o5.contour_list)) {
 		contourstack2centroid($o1, $o2, $o3, $o4, $o5)
 		return
 	}
-	mean = swc.sections.object(0).contourcenter($o1, $o2, $o3)
+	sec = swc.sections.object(0)
+	mean = sec.contourcenter($o1, $o2, $o3)
     if (g != nil) {
 	g.beginline(6,1)
 	for i=0, $o1.size-1 {
@@ -1307,6 +1317,14 @@ if (g != nil) g.line(tobj.x[0], tobj.x[1]) g.flush
 	for i=1,3 { $oi = pts.getrow(i-1) }
 //	print d  d.printf  print rad rad.printf
 //	print side2 side2.printf  print rad2  rad2.printf
+
+	// store the center of the processed contour for later
+	// updating of child logical connection to center of section
+	j = $o1.size-1
+	for i = 1, 3 {
+		mean.x[i-1] = ($oi.x[0] + $oi.x[j])/2
+	}
+        sec.processed_contour_center = mean.c()
 }
 
 proc contourstack2centroid() {local i, j, area, d  localobj c

share/lib/hoc/import3d/import3d_sec.hoc

@@ -16,6 +16,11 @@ public stk_triang_vec, stk_triang_area, is_subsidiary
 public volatile2, contourcenter, ztrans, approximate_contour_by_circle
 public pl_point, insrt, set_pt, stk_center, accurate_triangle_area
 objref raw, xyz, d, g, parentsec, contour_list, this, stk_triang_vec
+// processed_contour_center vector introduced because it may differ
+// from the raw contour center
+public processed_contour_center
+objref processed_contour_center
+
 proc init() {
 	is_subsidiary = 0
 	ztrans = 0
@@ -184,7 +189,6 @@ proc rotate() {
     }
 }
 
-
 // a utility function
 obfunc contourcenter() {local i localobj mean, pts, perim, d
 	// convert contour defined by $o1, $o2, $o3 vectors to

src/nrnpython/nrnpy_hoc.cpp

@@ -2864,9 +2864,10 @@ extern "C" NRN_EXPORT PyObject* get_plotshape_data(PyObject* sp) {
     void* that = pho->ho_->u.this_pointer;
 #if HAVE_IV
     IFGUI
-        spi = ((ShapePlot*) that);
-    } else {
-        spi = ((ShapePlotData*) that);
+    spi = ((ShapePlot*) that);
+}
+else {
+    spi = ((ShapePlotData*) that);
     ENDGUI
 #else
     spi = ((ShapePlotData*) that);

test/CMakeLists.txt

@@ -313,7 +313,8 @@ if(NRN_ENABLE_PYTHON)
         GROUP hoctests
         NAME ${name}_${ext} ${${ext}_preload} # PRELOAD_SANITIZER for Python
         COMMAND ${${ext}_exe} "${hoc_script}"
-        SCRIPT_PATTERNS "${hoc_script}" "tests/${name}.json" ${${ext}test_utils})
+        SCRIPT_PATTERNS "${hoc_script}" "tests/${name}.json" "tests/${name}.asc"
+                        ${${ext}test_utils})
     endforeach()
   endforeach()
 

test/hoctests/tests/test_pt3dstyle.asc

@@ -0,0 +1,24 @@
+("CellBody"
+  (Color Red)
+  (CellBody)
+  (3.80077 3.41923 0 0)  ; 1, 1
+  (3.81077 1.71923 0 0)  ; 1, 2
+  (6.30077 -1.15077 0 0)  ; 1, 3
+  (5.79077 -3.76077 0 0)  ; 1, 4
+  (2.48077 -6.86077 0 0)  ; 1, 5
+  (-0.849229 -8.24077 0 0)  ; 1, 6
+  (-4.37923 -7.22077 0 0)  ; 1, 7
+  (-5.62923 -4.94077 0 0)  ; 1, 8
+  (-5.19923 -0.95077 0 0)  ; 1, 9
+  (-3.06923 4.74923 0 0)  ; 1, 10
+  (-1.70923 6.51923 0 0)  ; 1, 11
+  (-2.10923 7.95923 0 0)  ; 1, 12
+  (0.760771 8.75923 0 0)  ; 1, 13
+);
+
+( (Color Blue)
+  (Axon)
+  (-1.10012 -6.51191 1.75185 1.33)
+  (-1.39509 -8.25791 2.22157 1.33)
+  (-2.03149 -16.6016 2.41259 0.66)
+);

test/hoctests/tests/test_pt3dstyle.py

@@ -0,0 +1,55 @@
+from neuron import h
+from math import isclose
+import os
+
+
+class Cell:
+    def __init__(self, id):
+        self.id = id
+
+    def __str__(self):
+        return "Cell_%d" % self.id
+
+
+cell = Cell(0)
+h.load_file("stdrun.hoc")
+h.load_file("import3d.hoc")
+nl = h.Import3d_Neurolucida3()
+nl.quiet = 1
+dir_path = os.path.dirname(os.path.realpath(__file__))
+fname = os.path.join(dir_path, "test_pt3dstyle.asc")
+nl.input(fname)
+import_neuron = h.Import3d_GUI(nl, 0)
+import_neuron.instantiate(cell)
+
+
+def logcon(s):
+    lcf = tuple([h.ref(0.0) for _ in range(3)])
+    lc = h.pt3dstyle(1, *lcf, sec=s)
+    return lc, [ref[0] for ref in lcf]
+
+
+def vec3d(s):
+    vecs = [[] for _ in range(4)]  # x, y ,z, d
+    for i, f in enumerate([h.x3d, h.y3d, h.z3d, h.diam3d]):
+        for j in range(s.n3d()):
+            vecs[i].append(f(j))
+    return vecs
+
+
+def allpts():
+    return [vec3d(s) for s in h.allsec()]
+
+
+stdpts = allpts()
+stdlogcon = logcon(cell.axon[0])
+
+h.define_shape()
+
+assert stdpts == allpts()
+# The logical connection is only accurate to float32 resolution
+print(stdlogcon)
+print(logcon(cell.axon[0]))
+# assert stdlogcon == logcon(cell.axon[0])
+for i, val in enumerate(logcon(cell.axon[0])[1]):
+    assert isclose(stdlogcon[1][i], val, rel_tol=1e-7)