Skip to content

Commit

Permalink
Fixes to better handl HT model changes and assignment of concInit
Browse files Browse the repository at this point in the history
  • Loading branch information
@upibhalla
upibhalla committed Sep 30, 2023
1 parent 8282172 commit 9bea8f8
Showing 1 changed file with 55 additions and 36 deletions.
91 changes: 55 additions & 36 deletions simWrapHillTau.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -117,8 +117,12 @@ def _scaleOneParam( self, params ):
dictReac["Amod"] = reac.Amod

def deleteItems( self, itemsToDelete ):
# This operates at the level of the JSON dict. We then have to
# rebuild the model.
# This accumulates a list of objects to delete, which is then
# applied to the model once it is built.
# Note that we silently ignore requests to delete nonexistent
# objects, or objects that are missing from the map.
# Logic is that if the object doesn't exist here, it doesn't matter
# if the experiment wants to delete it for some other model.
for ( _entity, change ) in itemsToDelete:
if change != 'delete':
continue
Expand All @@ -129,18 +133,21 @@ def deleteItems( self, itemsToDelete ):
if objList:
for obj in objList:
self.deleteList.append( obj )
elif self.ignoreMissingObj:
else:
if not self.silent:
print( "Alert: simWrapHillTau::deleteItems: entity '{}' not found".format( _entity ) )
else:
raise SimError( "SimWrapHillTau::deleteItems: Entity '{}' not found".format( _entity ) )

def subsetItems( self, _modelSubset ):
# This builds up a 'saveList' of items to be preserved for
# calculation.
# If a subset entry is a group, save all its reactions and eqns.
# If a subset entry is a reaction or eqn, save it.
# Don't need to delete anything, just disable unused reacs.
# If a subset doesn't exist in the model, ignore the request
# without raising an error.
# The reasoning is that the subsetted object is implicitly there,
# so it is safe as long as we don't try to assign anything to it.
# If we try to use it as a stim or readout other functions will
# flag it.
self.saveList = []
for i in _modelSubset:
objList = self.modelLookup.get(i)
Expand All @@ -151,12 +158,9 @@ def subsetItems( self, _modelSubset ):
# The modifySched func recognizes if i is the parent grp
self.saveList.append( i )
# Could do recursive stuff here if need groups in groups.

elif self.ignoreMissingObj:
else:
if not self.silent:
print( "Alert: simWrapHillTau::subsetItems: entity '{}' not found".format( i ) )
else:
raise SimError( "SimWrapHillTau::subsetItems: Entity '{}' not found".format( i ) )

def pruneDanglingObj( self, erSPlist ): # Should be clean already
return
Expand All @@ -166,26 +170,50 @@ def changeParams( self, params ):
simWrapHillTau::changeParams( self, params )
This changes param values.
It operates directly on the json dict.
It is meant to be called BEFORE the modelLookup is built.
It is meant to be called AFTER the modelLookup is built. It needs
to look up and convert names from the expt file to the model Json.
It does some nasty things for assignments to eqns, which only
permit string assignments in the hillTau schema.
If the modified object doesn't exist in the model, raise an error.
'''
for ( entity, field, value) in params:
for ( exptEntity, field, value) in params:
mm = self.modelLookup.get( exptEntity )
if not mm:
raise SimError( "SimWrapHillTau::changeParams: '{}' not found on lookup.".format( exptEntity ) )
entity = mm[0]
#print( "changing entity {} to {}.{}={}".format( exptEntity, entity, field, value ) )
for jg in self.jsonDict["Groups"].values():
if field == "conc" or field == "concInit":
s = jg.get( "Species" )
if s and entity in s:
s[entity] = value
#print("Changing {} of '{}' to {}".format( field, entity, value ) )
#print("Trying {} of '{}' to {}".format( field, entity, value ) )
rr = jg.get( "Reacs" )
if rr and entity in rr:
rr[entity]["concInit"] = value
#print("Changing reac {} of '{}' to {}".format( field, entity, value ) )
continue
ss = jg.get( "Species" )
if ss and entity in ss:
ss[entity] = value
#print("Changing species {} of '{}' to {}".format( field, entity, value ) )
continue
ee = jg.get( "Eqns" )
if ee and entity in ee:
ee[entity] = "concInit=" + str( value )
#print("Changing eqn {} of '{}' to {}".format( field, entity, ee[entity] ) )
continue
elif field == "isBuffered" and value == 1:
r = jg.get( "Reacs" )
if r and entity in r:
# This simply removes the entity from the eval queue
# self.deleteList.append( entity )
r[entity]["isBuffered"] = 1
continue
#self.setField( entity, "isBuffered", 1 )
else:
e = jg.get( "Eqns" )
if e and entity in e:
self.deleteList.append( entity )
continue
# Ignore it. We assume that if it is buffered then concInit is set or is going to be set.
#self.deleteList.append( entity )
#if len( self.deleteList ) > 0:
# self.model.modifySched( saveList = [], deleteList = self.deleteList )

Expand Down Expand Up @@ -236,7 +264,6 @@ def loadModelFile( self, fname, modifyFunc, scaleParam, dumpFname, paramFname ):
scaleParam = self.scaleNamedConsts( scaleParam )
qs = hillTau.getQuantityScale( self.jsonDict )
hillTau.scaleDict( self.jsonDict, qs )
self.extendObjMap() # Extends objects from jsonDict into objMap
# modifyFunc comes back as deleteItems, subsetItems, prune, changeParams
self.buildModelLookup( self.objMap )
modifyFunc( {}, "" ) # Callback.
Expand All @@ -262,25 +289,8 @@ def loadModelFile( self, fname, modifyFunc, scaleParam, dumpFname, paramFname ):
self.loadtime += time.time() - t0
return


def extendObjMap( self ):
om = self.objMap
for key, val in self.jsonDict["Groups"].items():
# Only put in the groups which have not been remapped.
if not key in om:
om[key] = [key]
if "Species" in val:
for i in val["Species"]:
if not i in om:
om[i] = [i]
if "Reacs" in val:
for i in val["Reacs"]:
if not i in om:
om[i] = [i]

def buildModelLookup( self, objMap ):
# All Mols are keys in modelLookup, plus whatever objMap sets.
# We ensure that only valid objects are keys.
# Keys must refer to valid objects
for key, val in objMap.items():
v = val[0]
self.modelLookup[key] = val
Expand Down Expand Up @@ -380,12 +390,21 @@ def setField( self, objName, field, value ):
if field in ['conc', 'concInit']:
#print( "{}.{} = {}".format( objName, field, value ) )
if objName in self.model.molInfo:
'''
idx = self.model.molInfo[objName].index
self.model.concInit[idx] = self.model.conc[ idx ]= value
print( "Setting {}[{}] concInit to {}".format( objName, idx, value ) )
'''
if field == 'conc':
self.model.conc[ self.model.molInfo[objName].index ]= value
elif field == 'concInit':
#print( "Setting {} concInit to {}".format( objName, value ) )
self.model.concInit[ self.model.molInfo[objName].index ]= value
else:
raise SimError( "SimWrapHillTau::setField: Unknown mol {}".format( objName ) )
elif field == "isBuffered" and objName in self.model.eqnInfo:
eqn = self.model.eqnInfo[ objName ]
eqn.isBuffered = value
elif field in ['KA', 'tau', 'tau2', 'baseline', 'gain', 'Kmod', 'Amod', "isBuffered"]:
if objName in self.model.reacInfo:
reac = self.model.reacInfo[objName]
Expand Down

0 comments on commit 9bea8f8

Please sign in to comment.