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Removing possibility of ignoring compartment volume

Andrej %!s(int64=2) %!d(string=hai) anos
pai
achega
0b100fff9c
Modificáronse 1 ficheiros con 6 adicións e 9 borrados
  1. 6 9
      pythonScripts/cModel.py

+ 6 - 9
pythonScripts/cModel.py

@@ -29,7 +29,7 @@ class model:
       except KeyError:
          return 's'
 
-   def bind(self,src,target,qName,pcName,useVolume=0):
+   def bind(self,src,target,qName,pcName):
       
 
       #establish a flow from source compartment to the target
@@ -37,7 +37,7 @@ class model:
       #the source equation (where we subtract the current)
       #in fact, this is the diagonal element
       #get volume names
-      srcVName=self.getVolumePar(src,useVolume)
+      srcVName=self.getVolumePar(src)
       #generate coupling object (w/derivatives)    
       pSrc=self.couplingObject(-1,qName,pcName,srcVName)
       #this includes derivatives and value!
@@ -49,7 +49,7 @@ class model:
 
       #the target equation (where we add the current)
       #get volume names
-      targetVName=self.getVolumePar(target,useVolume)
+      targetVName=self.getVolumePar(target)
       #generate coupling object
       pTarget=self.couplingObject(1,qName,pcName,targetVName)
       #equation is for target compartment, but binding for source
@@ -98,11 +98,9 @@ class model:
       #derivatives is the combination of the above
             
 
-   def getVolumePar(self,compartment,useVolume=1):
+   def getVolumePar(self,compartment):
       #returnis volume name, if found and useVolume is directed, 
       #or a standard parameter one
-      if not useVolume:
-         return "one"
       try:
          return self.mod["volumes"][compartment]
          #parV=self.mod["parameters"][parVName]
@@ -286,7 +284,6 @@ class model:
       for b in self.mod['bindings']['diffusion']:
          #whether to scale transfer constants to organ volume
          #default is true, but changing here will assume no scaling
-         useVolume=1
          comps=b.split('->')
          try:
              pcParName=self.mod['partitionCoefficients'][b]
@@ -295,7 +292,7 @@ class model:
         
          kParName=self.mod['bindings']['diffusion'][b]
          #operate with names to allow for value/function/derived infrastructure
-         self.bind(comps[0],comps[1],kParName,pcParName,useVolume)
+         self.bind(comps[0],comps[1],kParName,pcParName)
          
       for q in self.mod['bindings']['flow']:
          comps=q.split('->')
@@ -318,7 +315,7 @@ class model:
                  flowParName=self.mod['flows'][qName]
                  #flowPar=pars[flowParName]
                  
-                 self.bind(cs,ct,flowParName,pcParName,1)
+                 self.bind(cs,ct,flowParName,pcParName)
                  
       self.build()