Cleaned up syntax for nsdfview and for rdesigneur outputFileList specifiers.

Author: upibhalla

python/rdesigneur/moogul.py

@@ -236,7 +236,6 @@ def firstDraw( self, mergeDisplays, rotation=0.0, elev=0.0, azim=0.0, center = [
                 self.doAutoscale()
             self.updateAxis()
         if self.viewIdx == (MooView.viewIdx-1):
-            print( "last View", self.viewIdx)
             self.graph = vp.graph( title = "Graph", xtitle = "Time (s)", ytitle = " Units here", width = 700, fast=False, align = "left" )
             self.graphPlot1 = vp.gcurve( color = vp.color.blue, interval=-1)
             #self.graphPlot1.data =  [[0,0], [1,1],[2,0],[3,4],[4,0], [5,1]]

python/rdesigneur/nsdfview.py

@@ -16,15 +16,22 @@ def __init__( self, path ):
         self.path = str( path, "utf-8" )
 
 class NsdfNeuronDataWrapper( moogul.DataWrapper ):
-    def __init__( self, nsdf, neuronName, field ):
-        if len( neuronName.split('/' ) ) != 2:
-            print( "Error: neuronName needs '/' between base and rel parts: ", objname )
-            assert( 0 )
+    def __init__( self, nsdf, path, field ):
         moogul.DataWrapper.__init__( self, field )
         self.nsdf_ = nsdf
-        self.neuronName_ = neuronName
-        self.objBase_ = neuronName.split( '/' )[0]
-        self.objRel_ = neuronName.split( '/' )[1]
+        self.path_ = path
+        spl = path.split( '/', 1 )
+        self.objBase_ = "%elec"
+        if len( spl ) > 1:  # Some relative path tree.
+            if spl[0] == "#":
+                self.objRel_ = "##[ISA=CompartmentBase]%" + spl[1].replace( '/', '%' )
+            else:
+                self.objRel_ = spl[0] + "%" + spl[1].replace( '/', '%' )
+        else:
+            if spl[0] == "#":
+                self.objRel_ = "##[ISA=CompartmentBase]"
+            else:
+                self.objRel_ = path   # No slashes in the string.
         self.field_ = field
         self.simTime_ = 0.0
         self.idx_ = 0
@@ -80,9 +87,18 @@ def __init__( self, nsdf, objname,  field ):
             assert( 0 )
         moogul.DataWrapper.__init__( self, field )
         self.nsdf_ = nsdf
-        self.objBase_ = objname.split( '/' )[0]
-        self.objRel_ = objname.split( '/' )[1]
-        
+        spl = objname.split( '/', 1 )
+        if len( spl ) > 1:  # Can't deal with case where we have /chem as base but multiple levels below it.
+            self.objBase_ = '%' + spl[0]
+            self.objRel_ = spl[1].replace( '/', '%' )
+            if self.objRel_[-1] != ']':  # put in wildcard, if none provided
+                self.objRel_ += '[]'
+        else:   # obj is direct child of /chem.
+            self.objBase_ = "%chem"
+            self.objRel_ = objname  # doesn't have any slashes either.
+            if self.objRel_[-1] != ']':  # put in wildcard, if none provided
+                self.objRel_ += '[]'
+
         self.field_ = field
         self.simTime_ = 0.0
         self.idx_ = 0

python/rdesigneur/rdesigneur.py

@@ -1021,24 +1021,23 @@ def _buildFileOutput( self ):
                 # Should check for duplication.
                 nsdfPath = fileBase.path + '/' + oname
                 if fentry.field in ["n", "conc"]:
-                    if fentry.basepath[:4] == 'chem': #chem itself as compt
-                        modelPath = self.modelPath
+                    modelPath = self.modelPath + "/chem" 
+                    basePath = modelPath + "/" + fentry.path
+                    if fentry.path[-1] in [']', '#']: # explicit index
+                        pathStr = basePath + "." + fentry.field
                     else:
-                        modelPath = self.modelPath + "/chem" 
-                    basePath = modelPath + "/" + fentry.basepath
-                    pathStr = basePath + '/' + fentry.relpath + "[]." + fentry.field
+                        pathStr = basePath + "[]." + fentry.field
                 else:
                     modelPath = self.modelPath + "/elec" 
-                    if fentry.basepath in ["elec", "#", "."]:
-                        fentry.basepath = "##[ISA=CompartmentBase]"
-                    elif fentry.basepath in ["spine", "SPINE", "head", "HEAD"]:
-                        fentry.basepath = "#head#[ISA=CompartmentBase]"
+                    spl = fentry.path.split('/')
+                    if spl[0] == "#":
+                        if len( spl ) == 1:
+                            fentry.path = "##[ISA=CompartmentBase]"
+                        else:
+                            fentry.path = "##[ISA=CompartmentBase]" + fentry.path[1:]
                     # Otherwise we use basepath as is.
-                    basePath = modelPath + "/" + fentry.basepath
-                    if fentry.relpath in [".", "/", "./"]:
-                        pathStr = basePath + "." + fentry.field
-                    else:
-                        pathStr = basePath + '/' + fentry.relpath + "." + fentry.field
+                    basePath = modelPath + "/" + fentry.path
+                    pathStr = basePath + "." + fentry.field
                 if not nsdfPath in nsdfBlocks:
                     self.nsdfPathList.append( nsdfPath )
                     nsdfBlocks[nsdfPath] = [pathStr]
@@ -1262,7 +1261,7 @@ def _buildStims( self ):
         }
         stims = moose.Neutral( self.modelPath + '/stims' )
         k = 0
-        # rstim class has {elecpath, geom_expr, relpath, field, expr}
+        # rstim class has {fname, path, field, dt, flush_steps }
         for i in self.stimList:
             pair = i.elecpath + " " + i.geom_expr
             dendCompts = self.elecid.compartmentsFromExpression[ pair ]
@@ -1965,10 +1964,12 @@ def convertArg( arg ):
 
 class rfile:
     def __init__( self,
-            fname = 'output.h5', basepath = 'elec', relpath = '.', field = 'Vm', dt = 1e-4, flushSteps = 200, start = 0.0, stop = -1.0, ftype = 'nsdf'):
+            fname = 'output.h5', path = 'soma', field = 'Vm', dt = 1e-4, flushSteps = 200, start = 0.0, stop = -1.0, ftype = 'nsdf'):
         self.fname = fname
-        self.basepath = basepath
-        self.relpath = relpath
+        self.path = path
+        if not field in knownFieldsDefault:
+            print( "Error: Field '{}' not known.".format( field ) )
+            assert( 0 )
         self.field = field
         self.dt = dt
         self.flushSteps = flushSteps
@@ -1977,11 +1978,12 @@ def __init__( self,
         self.ftype = self.fname.split(".")[-1]
         if not self.ftype in ["txt", "csv", "h5", "nsdf"]:
             print( "Error: output file format for ", fname , " not known")
+            assert( 0 )
         self.fname = self.fname.split("/")[-1]
 
     def printme( self ):
-        print( "{0}, {1}, {2}, {3}, {4}".format( 
-            self.fname, self.basepath, self.relpath, self.field, self.dt) )
+        print( "{0}, {1}, {2}, {3}".format( 
+            self.fname, self.path, self.field, self.dt) )
 
     @staticmethod
     def convertArg( arg ):