moogList properly handled

Author: analkumar2

python/rdesigneur/moogul.py

@@ -218,7 +218,7 @@ def drawForTheFirstTime( self, ax ):
 class MooNeuron( MooDrawable ):
     ''' Draws collection of line segments of defined dia and color'''
     def __init__( self,
-        neuronId,
+        mooObj,
         fieldInfo,
         field = 'Vm', 
         relativeObj = '.', 
@@ -235,12 +235,12 @@ def __init__( self,
                 colormap = colormap, lenScale = lenScale, 
                 diaScale = diaScale, autoscale = autoscale, 
                 valMin = valMin, valMax = valMax )
-        self.neuronId = neuronId
+        self.mooObj = mooObj
         self.updateCoords()
 
     def updateCoords( self ):
         ''' Obtains coords from the associated cell'''
-        self.compts_ = moose.wildcardFind( self.neuronId.path + "/#[ISA=CompartmentBase]" )
+        self.compts_ = self.mooObj
         # Matplotlib3d isn't able to do full rotations about an y axis,
         # which is what the NeuroMorpho models use, so
         # here we shuffle the axes around. Should be an option.

python/rdesigneur/rdesigneur.py

@@ -687,6 +687,56 @@ def _parseComptField( self, comptList, plotSpec, knownFields ):
         else:
             return comptList, kf[1]
 
+    # Returns vector of source objects, and the field to use. 
+    # Specifically for _buildMoogli() as there the coordinates of the compartments are needed.
+    # plotSpec is of the form
+    #   [ region_wildcard, region_expr, path, field, title]
+    def _MoogparseComptField( self, comptList, plotSpec, knownFields ):
+        # Put in stuff to go through fields if the target is a chem object
+        field = plotSpec.field
+        if not field in knownFields:
+            print("Warning: Rdesigneur::_parseComptField: Unknown field '{}'".format( field ) )
+            return (), ""
+
+        kf = knownFields[field] # Find the field to decide type.
+        # if kf[0] in ['CaConcBase', 'ChanBase', 'NMDAChan', 'VClamp']:
+        #     objList = self._collapseElistToPathAndClass( comptList, plotSpec.relpath, kf[0] )
+        #     return objList, kf[1]
+        if field in [ 'n', 'conc', 'volume']:
+            path = plotSpec.relpath
+            pos = path.find( '/' )
+            if pos == -1:   # Assume it is in the dend compartment.
+                path  = 'dend/' + path
+            pos = path.find( '/' )
+            chemCompt = path[:pos]
+            if chemCompt[-5:] == "_endo":
+                chemCompt = chemCompt[0:-5]
+            cc = moose.element( self.modelPath + '/chem/' + chemCompt)
+            voxelVec = []
+            temp = [ self._makeUniqueNameStr( i ) for i in comptList ]
+            #print( temp )
+            #print( "#####################" )
+            comptSet = set( temp )
+            #em = [ moose.element(i) for i in cc.elecComptMap ]
+            em = sorted( [ self._makeUniqueNameStr(i[0]) for i in cc.elecComptMap ] )
+            #print( em )
+            #print( "=================================================" )
+
+            voxelVec = [i for i in range(len( em ) ) if em[i] in comptSet ]
+            # Here we collapse the voxelVec into objects to plot.
+            allObj = moose.vec( self.modelPath + '/chem/' + plotSpec.relpath )
+            #print "####### allObj=", self.modelPath + '/chem/' + plotSpec[2]
+            if len( allObj ) >= len( voxelVec ):
+                objList = [ allObj[int(j)] for j in voxelVec]
+            else:
+                objList = []
+                print( "Warning: Rdesigneur::_parseComptField: unknown Object: '", plotSpec.relpath, "'" )
+            #print "############", chemCompt, len(objList), kf[1]
+            return objList, kf[1]
+
+        else:
+            return comptList, kf[1]
+
 
     def _buildPlots( self ):
         knownFields = {
@@ -769,8 +819,8 @@ def _buildMoogli( self ):
             pair = i.elecpath + " " + i.geom_expr
             dendCompts = self.elecid.compartmentsFromExpression[ pair ]
             spineCompts = self.elecid.spinesFromExpression[ pair ]
-            dendObj, mooField = self._parseComptField( dendCompts, i, knownFields )
-            spineObj, mooField2 = self._parseComptField( spineCompts, i, knownFields )
+            dendObj, mooField = self._MoogparseComptField( dendCompts, i, knownFields )
+            spineObj, mooField2 = self._MoogparseComptField( spineCompts, i, knownFields )
             assert( mooField == mooField2 )
             mooObj3 = dendObj + spineObj
             numMoogli = len( mooObj3 )

python/rdesigneur/rmoogli.py

@@ -39,7 +39,7 @@ def makeMoogli( rd, mooObj, args, fieldInfo ):
                 valMin = ymin, valMax = ymax )
         viewer.addDrawable( reacSystem )
     else:
-        neuron = moogul.MooNeuron( rd.elecid, fieldInfo,
+        neuron = moogul.MooNeuron( mooObj, fieldInfo,
                 field = mooField, relativeObj = relObjPath,
                 valMin = ymin, valMax = ymax )
         print( "min = {}, max = {}".format(ymin, ymax) )