diff --git a/moose-core/diffusion/Dsolve.cpp b/moose-core/diffusion/Dsolve.cpp
index b90fbc267e6d419b04b912ca5070af8919436df0..9f1fc45af0e0e566eec1971ca6060223552f19ef 100644
--- a/moose-core/diffusion/Dsolve.cpp
+++ b/moose-core/diffusion/Dsolve.cpp
@@ -422,7 +422,9 @@ void Dsolve::calcJnChan( const DiffJunction& jn, Dsolve* other, double dt )
double lastN = myN;
double otherN = otherDv.getN( j->second );
double chanN = chanDv.getN( j->first );
- double perm = myChan.permeability * chanN / NA;
+ // Stick in a conversion factor for the myN and otherN into
+ // concentrations. Note that SI is millimolar.
+ double perm = myChan.permeability * chanN * 1000.0 / NA;
myN = integ( myN, perm * myN/j->firstVol,
perm * otherN/j->secondVol, dt );
otherN += lastN - myN; // Mass consv
@@ -459,7 +461,9 @@ void Dsolve::calcOtherJnChan( const DiffJunction& jn, Dsolve* other, double dt )
double lastN = myN;
double otherN = otherDv.getN( j->second );
double chanN = chanDv.getN( j->second );
- double perm = otherChan.permeability * chanN / NA;
+ // Stick in a conversion factor for the myN and otherN into
+ // concentrations. Note that SI is millimolar.
+ double perm = otherChan.permeability * chanN * 1000.0 / NA;
myN = integ( myN, perm * myN/j->firstVol,
perm * otherN/j->secondVol, dt );
otherN += lastN - myN; // Mass consv
@@ -1130,7 +1134,7 @@ double Dsolve::getNinit( const Eref& e ) const
{
return pools_[ pid ].getNinit( vox );
}
- cout << "Warning: Dsolve::setNinit: Eref " << e << " out of range " <<
+ cout << "Warning: Dsolve::getNinit: Eref " << e << " out of range " <<
pools_.size() << ", " << numVoxels_ << "\n";
return 0.0;
}
diff --git a/moose-core/kinetics/ReadKkit.cpp b/moose-core/kinetics/ReadKkit.cpp
index 0b3824643f39d5650183ed4342d22a09942533f9..01254b62292d6a3cc1f2bdf92638e4c04dcadd3c 100644
--- a/moose-core/kinetics/ReadKkit.cpp
+++ b/moose-core/kinetics/ReadKkit.cpp
@@ -1195,6 +1195,7 @@ Id ReadKkit::buildChan( const vector< string >& args )
assert( chan != Id() );
string chanPath = clean.substr( 10 );
chanIds_[ chanPath ] = chan;
+ Id info = buildInfo( chan, chanMap_, args );
return chan;
}
diff --git a/moose-core/mesh/EndoMesh.cpp b/moose-core/mesh/EndoMesh.cpp
index 7902e3bded47f9e28f2473eeadbfed264d647fc8..e1e21dfdec33ec10d8ba5c9061e42b34f09c1fd6 100644
--- a/moose-core/mesh/EndoMesh.cpp
+++ b/moose-core/mesh/EndoMesh.cpp
@@ -23,6 +23,9 @@
#include "NeuroMesh.h"
#include "EndoMesh.h"
#include "../utility/numutil.h"
+
+static CubeMesh defaultParent;
+
const Cinfo* EndoMesh::initCinfo()
{
//////////////////////////////////////////////////////////////
@@ -137,7 +140,7 @@ static const Cinfo* endoMeshCinfo = EndoMesh::initCinfo();
//////////////////////////////////////////////////////////////////
EndoMesh::EndoMesh()
:
- parent_( 0 ),
+ parent_( &defaultParent ),
rPower_( 1.0 / 3.0 ),
rScale_( 0.5 ),
aPower_( 0.5 ),
@@ -263,7 +266,7 @@ unsigned int EndoMesh::getMeshDimensions( unsigned int fid ) const
/// Virtual function to return # of spatial dimensions of mesh
unsigned int EndoMesh::innerGetDimensions() const
{
- return 1;
+ return 3;
}
/// Virtual function to return volume of mesh Entry.
double EndoMesh::getMeshEntryVolume( unsigned int fid ) const
diff --git a/moose-core/python/moose/SBML/readSBML.py b/moose-core/python/moose/SBML/readSBML.py
index d9b0e90f0b531fb446123c5409c3b46e6bfd8de7..f8e74f7e13bdd9194b60dadc4f1f17a336fdd153 100644
--- a/moose-core/python/moose/SBML/readSBML.py
+++ b/moose-core/python/moose/SBML/readSBML.py
@@ -13,10 +13,11 @@
** copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
Created : Thu May 13 10:19:00 2016(+0530)
Version
-Last-Updated: Fri May 21 11:21:00 2018(+0530)
+Last-Updated: Fri Oct 26 11:21:00 2018(+0530)
By:HarshaRani
**********************************************************************/
2018
+Oct 26: - validator can be switchedoff by passing validate="off" while readSBML files
May 18: - cleanedup and connected cplx pool to correct parent enzyme
Jan 6: - only if valid model exists, then printing the no of compartment,pool,reaction etc
- at reaction level a check made to see if path exist while creating a new reaction
@@ -77,7 +78,7 @@ try:
except ImportError:
pass
-def mooseReadSBML(filepath, loadpath, solver="ee"):
+def mooseReadSBML(filepath, loadpath, solver="ee",validate="on"):
"""Load SBML model
"""
global foundLibSBML_
@@ -100,7 +101,10 @@ def mooseReadSBML(filepath, loadpath, solver="ee"):
filep = open(filepath, "r")
document = libsbml.readSBML(filepath)
tobecontinue = False
- tobecontinue = validateModel(document)
+ if validate == "on":
+ tobecontinue = validateModel(document)
+ else:
+ tobecontinue = True
if tobecontinue:
level = document.getLevel()
version = document.getVersion()
diff --git a/moose-core/python/moose/SBML/writeSBML.py b/moose-core/python/moose/SBML/writeSBML.py
index ec9d357f24443cb458957c06ebb66f452c5b2efb..a3d898d44c2b0c02d2f8e4f55404332f6ac9c86a 100644
--- a/moose-core/python/moose/SBML/writeSBML.py
+++ b/moose-core/python/moose/SBML/writeSBML.py
@@ -18,8 +18,11 @@ Last-Updated: Mon 30 Apr 15:10:00 2018(+0530)
**********************************************************************/
/****************************
2018
+Oct 16: CylMesh's comparment volume is written, but zeroth volex details are populated
+Oct 13: CylMesh are written to SBML with annotation field and only zeroth element/voxel (incase of cylMesh) of moose object is written
+Oct 1 : corrected the spell of CyclMesh-->CylMesh, negating the yaxis for kkit is removed
Apr 30: indentation corrected while writting annotation for enzymecomplex
-Jan 6: for Product_formation_, k3 units depends on noofSub, prd was passed which is fixed
+Jan 6 : for Product_formation_, k3 units depends on noofSub, prd was passed which is fixed
2017
Dec 15: If model path exists is checked
Enz cplx is written only if enz,cplx,sub, prd exist, a clean check is made
@@ -73,10 +76,12 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
if not moose.exists(modelpath):
return False, "Path doesn't exist"
elif moose.exists(modelpath):
- mObj = moose.wildcardFind(moose.element(modelpath).path+'/##[ISA=PoolBase]'+','+
- moose.element(modelpath).path+'/##[ISA=ReacBase]'+','+
- moose.element(modelpath).path+'/##[ISA=EnzBase]'+','+
- moose.element(modelpath).path+'/##[ISA=StimulusTable]')
+ checkCompt = moose.wildcardFind(modelpath+'/##[0][ISA=ChemCompt]')
+
+ mObj = moose.wildcardFind(moose.element(modelpath).path+'/##[0][ISA=PoolBase]'+','+
+ moose.element(modelpath).path+'/##[0][ISA=ReacBase]'+','+
+ moose.element(modelpath).path+'/##[0][ISA=EnzBase]'+','+
+ moose.element(modelpath).path+'/##[0][ISA=StimulusTable]')
for p in mObj:
if not isinstance(moose.element(p.parent),moose.CplxEnzBase):
if moose.exists(p.path+'/info'):
@@ -102,7 +107,7 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
cremodel_.setLengthUnits("length")
neutralNotes = ""
- specieslist = moose.wildcardFind(modelpath + '/##[ISA=PoolBase]')
+ specieslist = moose.wildcardFind(modelpath + '/##[0][ISA=PoolBase]')
if specieslist:
neutralPath = getGroupinfo(specieslist[0])
if moose.exists(neutralPath.path + '/info'):
@@ -117,18 +122,24 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
srcdesConnection = {}
writeUnits(cremodel_)
+
modelAnno = writeSimulationAnnotation(modelpath)
if modelAnno:
cremodel_.setAnnotation(modelAnno)
groupInfo = {}
+
compartexist, groupInfo = writeCompt(modelpath, cremodel_)
+
if compartexist == True:
species = writeSpecies( modelpath,cremodel_,sbmlDoc,sceneitems,groupInfo)
if species:
writeFunc(modelpath, cremodel_)
reacGroup = {}
+
writeReac(modelpath, cremodel_, sceneitems,groupInfo)
+
writeEnz(modelpath, cremodel_, sceneitems,groupInfo)
+
if groupInfo:
for key,value in groupInfo.items():
mplugin = cremodel_.getPlugin("groups")
@@ -152,6 +163,7 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
for values in value:
member = group.createMember()
member.setIdRef(values)
+
consistencyMessages = ""
SBMLok = validateModel(sbmlDoc)
if (SBMLok):
@@ -165,9 +177,9 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
return -1, consistencyMessages
else:
return False, "Atleast one compartment should exist to write SBML"
-
+
def writeEnz(modelpath, cremodel_, sceneitems,groupInfo):
- for enz in moose.wildcardFind(modelpath + '/##[ISA=EnzBase]'):
+ for enz in moose.wildcardFind(modelpath + '/##[0][ISA=EnzBase]'):
enzannoexist = False
enzGpnCorCol = " "
cleanEnzname = convertSpecialChar(enz.name)
@@ -630,7 +642,7 @@ def listofname(reacSub, mobjEnz):
def writeReac(modelpath, cremodel_, sceneitems,reacGroup):
- for reac in moose.wildcardFind(modelpath + '/##[ISA=ReacBase]'):
+ for reac in moose.wildcardFind(modelpath + '/##[0][ISA=ReacBase]'):
reacSub = reac.neighbors["sub"]
reacPrd = reac.neighbors["prd"]
if (len(reacSub) != 0 and len(reacPrd) != 0):
@@ -763,7 +775,7 @@ def writeReac(modelpath, cremodel_, sceneitems,reacGroup):
def writeFunc(modelpath, cremodel_):
- funcs = moose.wildcardFind(modelpath + '/##[ISA=Function]')
+ funcs = moose.wildcardFind(modelpath + '/##[0][ISA=Function]')
# if func:
foundFunc = False
for func in funcs:
@@ -824,7 +836,7 @@ def getGroupinfo(element):
# if /modelpath/Compartment/Group/Group1/Pool, then I check and get Group1
# And /modelpath is also a NeutralObject,I stop till I find Compartment
- while not mooseIsInstance(element, ["Neutral", "CubeMesh", "CyclMesh"]):
+ while not mooseIsInstance(element, ["Neutral", "CubeMesh", "CylMesh"]):
element = element.parent
return element
@@ -836,7 +848,7 @@ def idBeginWith(name):
return changedName
def findGroup_compt(melement):
- while not (mooseIsInstance(melement, ["Neutral","CubeMesh", "CyclMesh"])):
+ while not (mooseIsInstance(melement, ["Neutral","CubeMesh", "CylMesh"])):
melement = melement.parent
return melement
@@ -865,7 +877,7 @@ def convertSpecialChar(str1):
def writeSpecies(modelpath, cremodel_, sbmlDoc, sceneitems,speGroup):
# getting all the species
- for spe in moose.wildcardFind(modelpath + '/##[ISA=PoolBase]'):
+ for spe in moose.wildcardFind(modelpath + '/##[0][ISA=PoolBase]'):
sName = convertSpecialChar(spe.name)
comptVec = findCompartment(spe)
speciannoexist = False
@@ -977,14 +989,25 @@ def writeSpecies(modelpath, cremodel_, sbmlDoc, sceneitems,speGroup):
def writeCompt(modelpath, cremodel_):
# getting all the compartments
- compts = moose.wildcardFind(modelpath + '/##[ISA=ChemCompt]')
+ compts = moose.wildcardFind(modelpath + '/##[0][ISA=ChemCompt]')
groupInfo = {}
for compt in compts:
+ comptAnno = ""
comptName = convertSpecialChar(compt.name)
# converting m3 to litre
- size = compt.volume * pow(10, 3)
+ if isinstance(compt,moose.CylMesh):
+ size = (compt.volume/compt.numDiffCompts)*pow(10,3)
+ comptAnno = "<moose:CompartmentAnnotation><moose:Mesh>" + \
+ str(compt.className) + "</moose:Mesh>\n" + \
+ "<moose:numDiffCompts>" + \
+ str(compt.numDiffCompts)+ "</moose:numDiffCompts>\n" + \
+ "</moose:CompartmentAnnotation>"
+ else:
+ size = compt.volume * pow(10, 3)
ndim = compt.numDimensions
c1 = cremodel_.createCompartment()
+ if comptAnno:
+ c1.setAnnotation(comptAnno)
c1.setId(str(idBeginWith(comptName +
"_" +
str(compt.getId().value) +
@@ -993,11 +1016,12 @@ def writeCompt(modelpath, cremodel_):
"_")))
c1.setName(comptName)
c1.setConstant(True)
- c1.setSize(size)
+ c1.setSize(compt.volume*pow(10,3))
+ #c1.setSize(size)
c1.setSpatialDimensions(ndim)
c1.setUnits('volume')
#For each compartment get groups information along
- for grp in moose.wildcardFind(compt.path+'/##[TYPE=Neutral]'):
+ for grp in moose.wildcardFind(compt.path+'/##[0][TYPE=Neutral]'):
grp_cmpt = findGroup_compt(grp.parent)
try:
value = groupInfo[moose.element(grp)]
@@ -1011,6 +1035,7 @@ def writeCompt(modelpath, cremodel_):
else:
return False,groupInfo
# write Simulation runtime,simdt,plotdt
+
def writeSimulationAnnotation(modelpath):
modelAnno = ""
plots = ""
@@ -1027,7 +1052,8 @@ def writeSimulationAnnotation(modelpath):
modelAnno = modelAnno + "<moose:plotdt> " + \
str(mooseclock.dts[18]) + " </moose:plotdt>\n"
plots = ""
- graphs = moose.wildcardFind(modelpath + "/##[TYPE=Table2]")
+ graphs = moose.wildcardFind(modelpath + "/##[0][TYPE=Table2]")
+
for gphs in range(0, len(graphs)):
gpath = graphs[gphs].neighbors['requestOut']
if len(gpath) != 0:
@@ -1035,7 +1061,7 @@ def writeSimulationAnnotation(modelpath):
ori = q.path
name = convertSpecialChar(q.name)
graphSpefound = False
- while not(isinstance(moose.element(q), moose.CubeMesh)):
+ while not(isinstance(moose.element(q), moose.CubeMesh) or isinstance(moose.element(q),moose.CylMesh)):
q = q.parent
graphSpefound = True
if graphSpefound:
@@ -1046,6 +1072,7 @@ def writeSimulationAnnotation(modelpath):
else:
plots = plots + "; "+ori[ori.find(q.name)-1:len(ori)]
#plots = plots + "; /" + q.name + '/' + name
+
if plots != " ":
modelAnno = modelAnno + "<moose:plots> " + plots + "</moose:plots>\n"
modelAnno = modelAnno + "</moose:ModelAnnotation>"
diff --git a/moose-core/python/moose/genesis/writeKkit.py b/moose-core/python/moose/genesis/writeKkit.py
index 8fc6356902f2a4e07f5ecb586f34327d08a6b06c..4dc03c076b34ef859a9df055c440283c945aedc6 100644
--- a/moose-core/python/moose/genesis/writeKkit.py
+++ b/moose-core/python/moose/genesis/writeKkit.py
@@ -9,8 +9,11 @@ __version__ = "1.0.0"
__maintainer__ = "Harsha Rani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
-__updated__ = "Aug 8 2017"
+__updated__ = "Oct 23 2018"
+# 2018
+# Oct 16: Channels are written back to genesis
+# only zeroth element is taken for written back to genesis, this is true for CubeMesh and CylMesh
# 2017
# Aug 8 : All the moose object which doesn't have compartment are not written. Error message are appended
@@ -69,7 +72,7 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
cmin, xmin, ymin = 0, 0, 0
cmax, xmax, ymax = 1, 1, 1
- compt = moose.wildcardFind(modelpath+'/##[ISA=ChemCompt]')
+ compt = moose.wildcardFind(modelpath+'/##[0][ISA=ChemCompt]')
maxVol = estimateDefaultVol(compt)
positionInfoExist = True
if compt:
@@ -108,16 +111,19 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
enzList,error = writeEnz(modelpath,f,sceneitems)
errors = errors+error
- error = writeSumtotal(modelpath,f)
+ chanList, error = writeConcChan(modelpath,f,sceneitems)
errors = errors+error
error = writeStimulus(modelpath,f)
errors = errors+error
+ error = writeSumtotal(modelpath,f)
+ errors = errors+error
+
#writeSumtotal(modelpath,f)
f.write("simundump xgraph /graphs/conc1 0 0 99 0.001 0.999 0\n"
"simundump xgraph /graphs/conc2 0 0 100 0 1 0\n")
- tgraphs = moose.wildcardFind(modelpath+'/##[ISA=Table2]')
+ tgraphs = moose.wildcardFind(modelpath+'/##[0][ISA=Table2]')
first, second = " ", " "
if tgraphs:
first,second = writeplot(tgraphs,f)
@@ -133,6 +139,7 @@ def mooseWriteKkit( modelpath, filename, sceneitems={}):
"simundump xtext /file/notes 0 1\n")
storeReacMsg(reacList,f)
storeEnzMsg(enzList,f)
+ storeChanMsg(chanList,f)
if tgraphs:
storePlotMsgs(tgraphs,f)
writeFooter1(f)
@@ -171,7 +178,7 @@ def calPrime(x):
def storeCplxEnzMsgs( enz, f ):
for sub in enz.neighbors["subOut"]:
- s = "addmsg /kinetics/" + trimPath( sub ) + " /kinetics/" + trimPath(enz) + " SUBSTRATE n \n";
+ s = "addmsg /kinetics/" + trimPath( moose.element(sub) ) + " /kinetics/" + trimPath(enz) + " SUBSTRATE n \n";
s = s+ "addmsg /kinetics/" + trimPath( enz ) + " /kinetics/" + trimPath( sub ) + " REAC sA B \n";
f.write(s)
for prd in enz.neighbors["prd"]:
@@ -206,9 +213,72 @@ def storeEnzMsg( enzList, f):
else:
storeCplxEnzMsgs( enz, f )
+def storeChanMsg(chanList,f):
+ for channel in chanList:
+ for chanOL in channel.neighbors['out']:
+ eo = "addmsg /kinetics/" + trimPath(moose.element(channel)) + " /kinetics/" + trimPath(moose.element(chanOL))+ " REAC B A \n";
+ eo = eo +"addmsg /kinetics/" + trimPath(moose.element(chanOL)) + " /kinetics/"+trimPath(moose.element(channel))+" PRODUCT n vol \n";
+ f.write(eo)
+
+ for chanIL in channel.neighbors['in']:
+ ei = "addmsg /kinetics/" + trimPath(moose.element(channel)) + " /kinetics/" + trimPath(moose.element(chanIL))+ " REAC A B \n";
+ ei = ei +"addmsg /kinetics/" + trimPath(moose.element(chanIL)) + " /kinetics/"+trimPath(moose.element(channel))+" SUBSTRATE n vol \n";
+ f.write(ei)
+
+ for chanSNC in channel.neighbors['setNumChan']:
+ cff = "addmsg /kinetics/"+trimPath(moose.element(chanSNC))+ " /kinetics/"+trimPath(moose.element(channel))+ " NUMCHAN n \n"
+ f.write(cff)
+
+def writeConcChan(modelpath,f,sceneitems):
+ error = ""
+ concChanList = moose.wildcardFind(modelpath+'/##[0][ISA=ConcChan]')
+ for cChan in concChanList:
+ if findCompartment(cChan) == moose.element('/'):
+ error = error + " \n "+cChan.path+ " doesn't have compartment ignored to write to genesis"
+ else:
+ x = random.randrange(0,10)
+ y = random.randrange(0,10)
+ textcolor = ""
+ color = ""
+ if len(moose.element(cChan).neighbors['setNumChan']) == 1:
+ chanParent = moose.element(moose.element(cChan).neighbors['setNumChan'][0])
+
+ if not (isinstance(chanParent,moose.PoolBase)):
+ print(" raise exception Channel doesn't have pool as parent %s",moose.element(cChan).path)
+ return False,"raise exception Channel doesn't have pool as parent"
+ else:
+ vol = chanParent.volume * NA * 1e-3;
+
+ cinfo = cChan.path+'/info'
+ if moose.exists(cinfo):
+ x = moose.Annotator(cinfo).getField('x')
+ y = moose.Annotator(cinfo).getField('y')
+ #x = sceneitems[cChan]['x']
+ #y = sceneitems[cChan]['y']
+ color = moose.Annotator(cinfo).getField('color')
+ color = getColorCheck(color,GENESIS_COLOR_SEQUENCE)
+
+ textcolor = moose.Annotator(cinfo).getField('textColor')
+ textcolor = getColorCheck(textcolor,GENESIS_COLOR_SEQUENCE)
+ else:
+ error = error + "\n x and y co-ordinates are not specified for `" + cChan.name+ "` zero will be assigned \n "
+ if color == "" or color == " ":
+ color = getRandColor()
+ if textcolor == "" or textcolor == " ":
+ textcolor = getRandColor()
+ f.write("simundump kchan /kinetics/" + trimPath(cChan)+ " " + str(int(1)) + " " + str(cChan.permeability)+ " " +
+ str(int(0)) + " " +
+ str(int(0)) + " " +
+ str(int(0)) + " " +
+ str(int(0)) + " " +
+ str("") + " " +
+ str(textcolor) + " " + str(color) + " \"\"" +
+ " " + str(int(x)) + " " + str(int(y)) + " "+str(int(0))+"\n")
+
+ return concChanList,error
def writeEnz( modelpath,f,sceneitems):
error = ""
- enzList = moose.wildcardFind(modelpath+'/##[ISA=EnzBase]')
+ enzList = moose.wildcardFind(modelpath+'/##[0][ISA=EnzBase]')
for enz in enzList:
if findCompartment(enz) == moose.element('/'):
error = error + " \n "+enz.path+ " doesn't have compartment ignored to write to genesis"
@@ -313,7 +383,7 @@ def storeReacMsg(reacList,f):
def writeReac(modelpath,f,sceneitems):
error = ""
- reacList = moose.wildcardFind(modelpath+'/##[ISA=ReacBase]')
+ reacList = moose.wildcardFind(modelpath+'/##[0][ISA=ReacBase]')
for reac in reacList:
if findCompartment(reac) == moose.element('/'):
error = error + " \n "+reac.path+ " doesn't have compartment ignored to write to genesis"
@@ -385,7 +455,7 @@ def trimPath(mobj):
def writeSumtotal( modelpath,f):
error = ""
- funclist = moose.wildcardFind(modelpath+'/##[ISA=Function]')
+ funclist = moose.wildcardFind(modelpath+'/##[0][ISA=Function]')
s = ""
for func in funclist:
fInfound = True
@@ -420,7 +490,7 @@ def writeSumtotal( modelpath,f):
def writeStimulus(modelpath,f):
error = ""
- if len(moose.wildcardFind(modelpath+'/##[ISA=StimulusTable]')):
+ if len(moose.wildcardFind(modelpath+'/##[0][ISA=StimulusTable]')):
error = error +'\n StimulusTable is not written into genesis. This is in Todo List'
return error
@@ -501,7 +571,8 @@ def writePool(modelpath,f,volIndex,sceneitems):
error = ""
color = ""
textcolor = ""
- for p in moose.wildcardFind(modelpath+'/##[ISA=PoolBase]'):
+
+ for p in moose.wildcardFind(modelpath+'/##[0][ISA=PoolBase]'):
if findCompartment(p) == moose.element('/'):
error = error + " \n "+p.path+ " doesn't have compartment ignored to write to genesis"
else:
@@ -541,9 +612,8 @@ def writePool(modelpath,f,volIndex,sceneitems):
color = getColorCheck(color,GENESIS_COLOR_SEQUENCE)
textcolor = moose.Annotator(pinfo).getField('textColor')
textcolor = getColorCheck(textcolor,GENESIS_COLOR_SEQUENCE)
-
-
- geometryName = volIndex[p.volume]
+ poolsCmpt = findCompartment(p)
+ geometryName = volIndex[float(poolsCmpt.volume)]
volume = p.volume * NA * 1e-3
if color == "" or color == " ":
color = getRandColor()
@@ -616,6 +686,10 @@ def writeCompartment(modelpath,compts,f):
l = len(compts)
geometry = ""
for compt in compts:
+ # if isinstance(compt,moose.CylMesh):
+ # print " 1 "
+ # size = (compt.volume/compt.numDiffCompts)
+ # else:
size = compt.volume
ndim = compt.numDimensions
vecIndex = l-i-1
@@ -624,17 +698,18 @@ def writeCompartment(modelpath,compts,f):
y = ymax+1
if vecIndex > 0:
geometry = geometry+"simundump geometry /kinetics" + "/geometry[" + str(vecIndex) +"] 0 " + str(size) + " " + str(ndim) + " sphere " +" \"\" white black "+ str(int(x)) + " " +str(int(y)) +" 0\n";
- volIndex[size] = "/geometry["+str(vecIndex)+"]"
+ volIndex[float(size)] = "/geometry["+str(vecIndex)+"]"
else:
+
geometry = geometry+"simundump geometry /kinetics" + "/geometry 0 " + str(size) + " " + str(ndim) + " sphere " +" \"\" white black " + str(int(x)) + " "+str(int(y))+ " 0\n";
- volIndex[size] = "/geometry"
- f.write(geometry)
+ volIndex[float(size)] = "/geometry"
+ f.write(geometry)
writeGroup(modelpath,f)
return volIndex
def writeGroup(modelpath,f):
ignore = ["graphs","moregraphs","geometry","groups","conc1","conc2","conc3","conc4","model","data","graph_0","graph_1","graph_2","graph_3","graph_4","graph_5"]
- for g in moose.wildcardFind(modelpath+'/##[TYPE=Neutral]'):
+ for g in moose.wildcardFind(modelpath+'/##[0][TYPE=Neutral]'):
if not g.name in ignore:
if trimPath(g) != None:
x = xmin+1
@@ -705,12 +780,12 @@ def writeNotes(modelpath,f):
notes = ""
#items = moose.wildcardFind(modelpath+"/##[ISA=ChemCompt],/##[ISA=ReacBase],/##[ISA=PoolBase],/##[ISA=EnzBase],/##[ISA=Function],/##[ISA=StimulusTable]")
items = []
- items = moose.wildcardFind(modelpath+"/##[ISA=ChemCompt]") +\
- moose.wildcardFind(modelpath+"/##[ISA=PoolBase]") +\
- moose.wildcardFind(modelpath+"/##[ISA=ReacBase]") +\
- moose.wildcardFind(modelpath+"/##[ISA=EnzBase]") +\
- moose.wildcardFind(modelpath+"/##[ISA=Function]") +\
- moose.wildcardFind(modelpath+"/##[ISA=StimulusTable]")
+ items = moose.wildcardFind(modelpath+"/##[0][ISA=ChemCompt]") +\
+ moose.wildcardFind(modelpath+"/##[0][ISA=PoolBase]") +\
+ moose.wildcardFind(modelpath+"/##[0][ISA=ReacBase]") +\
+ moose.wildcardFind(modelpath+"/##[0][ISA=EnzBase]") +\
+ moose.wildcardFind(modelpath+"/##[0][ISA=Function]") +\
+ moose.wildcardFind(modelpath+"/##[0][ISA=StimulusTable]")
for item in items:
if moose.exists(item.path+'/info'):
info = item.path+'/info'
@@ -741,4 +816,4 @@ if __name__ == "__main__":
if written:
print(" file written to ",output)
else:
- print(" could be written to kkit format")
+ print(" could be written to kkit format")
\ No newline at end of file
diff --git a/moose-core/python/moose/moose.py b/moose-core/python/moose/moose.py
index 069d43b9990f019dbcce29d3adc493d1b75d8ff6..a55bc7be1f1c6b86d36b838d68a7be7b9e245d17 100644
--- a/moose-core/python/moose/moose.py
+++ b/moose-core/python/moose/moose.py
@@ -122,7 +122,7 @@ known_types = ['void',
'melement'] + sequence_types
# SBML related functions.
-def mooseReadSBML(filepath, loadpath, solver='ee'):
+def mooseReadSBML(filepath, loadpath, solver='ee',validate="on"):
"""Load SBML model.
keyword arguments: \n
@@ -134,7 +134,7 @@ def mooseReadSBML(filepath, loadpath, solver='ee'):
"""
global sbmlImport_
if sbmlImport_:
- return _readSBML.mooseReadSBML( filepath, loadpath, solver )
+ return _readSBML.mooseReadSBML( filepath, loadpath, solver,validate )
else:
print( sbmlError_ )
return False
@@ -222,7 +222,7 @@ def mergeChemModel(src, des):
return False
# NML2 reader and writer function.
-def mooseReadNML2( modelpath ):
+def mooseReadNML2( modelpath, verbose = False ):
"""Read NeuroML model (version 2) and return reader object.
"""
global nml2Import_
@@ -230,7 +230,7 @@ def mooseReadNML2( modelpath ):
mu.warn( nml2ImportError_ )
raise RuntimeError( "Could not load NML2 support." )
- reader = _neuroml2.NML2Reader( )
+ reader = _neuroml2.NML2Reader( verbose = verbose )
reader.read( modelpath )
return reader
diff --git a/moose-core/python/moose/neuroml2/reader.py b/moose-core/python/moose/neuroml2/reader.py
index 6a9dec0fafb5d0574cfa7e196ae7b5a35d7c90fa..2f2e2d85c8c35c5b227b5e436fd4c39c26521409 100644
--- a/moose-core/python/moose/neuroml2/reader.py
+++ b/moose-core/python/moose/neuroml2/reader.py
@@ -33,13 +33,6 @@ import moose.utils as mu
from .units import SI
-def _unique( ls ):
- res = [ ]
- for l in ls:
- if l not in res:
- res.append( l )
- return res
-
def _unique( ls ):
res = [ ]
for l in ls:
@@ -134,6 +127,7 @@ class NML2Reader(object):
self.pop_to_cell_type = {}
self.seg_id_to_comp_name = {}
self.paths_to_chan_elements = {}
+ self.network = None
def read(self, filename, symmetric=True):
filename = os.path.realpath( filename )
@@ -146,9 +140,9 @@ class NML2Reader(object):
if len(self.doc.networks)>=1:
self.network = self.doc.networks[0]
-
moose.celsius = self._getTemperature()
+
self.importConcentrationModels(self.doc)
self.importIonChannels(self.doc)
self.importInputs(self.doc)
@@ -163,10 +157,13 @@ class NML2Reader(object):
mu.info("Read all from %s"%filename)
def _getTemperature(self):
- if self.network.type=="networkWithTemperature":
- return SI(self.network.temperature)
- else:
- return 0 # Why not, if there's no temp dependence in nml..?
+ if self.network is not None:
+ if self.network.type=="networkWithTemperature":
+ return SI(self.network.temperature)
+ else:
+ # Why not, if there's no temp dependence in nml..?
+ return 0
+ return SI('25')
def getCellInPopulation(self, pop_id, index):
return self.cells_in_populations[pop_id][index]
@@ -407,11 +404,8 @@ class NML2Reader(object):
mu.info("Using %s to evaluate rate"%ct.name)
rate = []
for v in tab:
- vals = pynml.evaluate_component(ct
- , req_variables =
- {'v':'%sV'%v,'vShift':vShift,'temperature':self._getTemperature()}
- )
- # mu.info vals
+ req_vars = {'v':'%sV'%v,'vShift':vShift,'temperature':self._getTemperature()}
+ vals = pynml.evaluate_component(ct, req_variables = req_vars)
if 'x' in vals:
rate.append(vals['x'])
if 't' in vals:
@@ -420,6 +414,9 @@ class NML2Reader(object):
rate.append(vals['r'])
return np.array(rate)
+ print( "[WARN ] Could not determine rate: %s %s %s" %(ratefn.type,vmin,vmax))
+ return np.array([])
+
def importChannelsToCell(self, nmlcell, moosecell, membrane_properties):
sg_to_segments = self._cell_to_sg[nmlcell]
for chdens in membrane_properties.channel_densities + membrane_properties.channel_density_v_shifts:
@@ -487,10 +484,11 @@ class NML2Reader(object):
def createHHChannel(self, chan, vmin=-150e-3, vmax=100e-3, vdivs=5000):
mchan = moose.HHChannel('%s/%s' % (self.lib.path, chan.id))
mgates = [moose.element(x) for x in [mchan.gateX, mchan.gateY, mchan.gateZ]]
- assert(len(chan.gate_hh_rates) <= 3) # We handle only up to 3 gates in HHCHannel
+ assert len(chan.gate_hh_rates)<=3, "We handle only up to 3 gates in HHCHannel"
if self.verbose:
mu.info('== Creating channel: %s (%s) -> %s (%s)'%(chan.id, chan.gate_hh_rates, mchan, mgates))
+
all_gates = chan.gates + chan.gate_hh_rates
for ngate, mgate in zip(all_gates,mgates):
if mgate.name.endswith('X'):
@@ -512,9 +510,7 @@ class NML2Reader(object):
# refering to tau_inf and m_inf??
fwd = ngate.forward_rate
rev = ngate.reverse_rate
-
self.paths_to_chan_elements['%s/%s'%(chan.id,ngate.id)] = '%s/%s'%(chan.id,mgate.name)
-
q10_scale = 1
if ngate.q10_settings:
if ngate.q10_settings.type == 'q10Fixed':
@@ -536,6 +532,7 @@ class NML2Reader(object):
if (fwd is not None) and (rev is not None):
alpha = self.calculateRateFn(fwd, vmin, vmax, vdivs)
beta = self.calculateRateFn(rev, vmin, vmax, vdivs)
+
mgate.tableA = q10_scale * (alpha)
mgate.tableB = q10_scale * (alpha + beta)
@@ -554,8 +551,9 @@ class NML2Reader(object):
tau = 1 / (alpha + beta)
if inf is not None:
inf = self.calculateRateFn(inf, vmin, vmax, vdivs)
- mgate.tableA = q10_scale * (inf / tau)
- mgate.tableB = q10_scale * (1 / tau)
+ if len(inf) > 0:
+ mgate.tableA = q10_scale * (inf / tau)
+ mgate.tableB = q10_scale * (1 / tau)
if self.verbose:
mu.info('%s: Created %s for %s'%(self.filename,mchan.path,chan.id))
@@ -589,7 +587,7 @@ class NML2Reader(object):
def importIonChannels(self, doc, vmin=-150e-3, vmax=100e-3, vdivs=5000):
if self.verbose:
- mu.info('%s : Importing the ion channels' % self.filename )
+ mu.info('%s: Importing the ion channels' % self.filename )
for chan in doc.ion_channel+doc.ion_channel_hhs:
if chan.type == 'ionChannelHH':
@@ -603,7 +601,7 @@ class NML2Reader(object):
self.nml_to_moose[chan] = mchan
self.proto_chans[chan.id] = mchan
if self.verbose:
- mu.info( self.filename + ' : Created ion channel %s for %s %s'%(
+ mu.info( self.filename + ': Created ion channel %s for %s %s'%(
mchan.path, chan.type, chan.id))
def importConcentrationModels(self, doc):
diff --git a/moose-core/python/rdesigneur/rdesigneur.py b/moose-core/python/rdesigneur/rdesigneur.py
index 492cb1802c31b6b614351578bceb0bcf58a50944..6ad93d02b89981d95b1bc215df7d6e8ecffce079 100644
--- a/moose-core/python/rdesigneur/rdesigneur.py
+++ b/moose-core/python/rdesigneur/rdesigneur.py
@@ -179,7 +179,7 @@ class rdesigneur:
self.elecid.numCompartments, "compartments and",
self.elecid.numSpines, "spines on",
len( self.cellPortionElist ), "compartments.")
- if hasattr( self , 'chemid' ):
+ if hasattr( self , 'chemid') and len( self.chemDistrib ) > 0:
dmstoich = moose.element( self.dendCompt.path + '/stoich' )
print("\tChem part of model has the following compartments: ")
for j in moose.wildcardFind( '/model/chem/##[ISA=ChemCompt]'):
@@ -948,7 +948,7 @@ rdesigneur.rmoogli.updateMoogliViewer()
}
stims = moose.Neutral( self.modelPath + '/stims' )
k = 0
- # Stimlist = [path, geomExpr, relPath, field, expr_string]
+ # rstim class has {elecpath, geom_expr, relpath, field, expr}
for i in self.stimList:
pair = i.elecpath + " " + i.geom_expr
dendCompts = self.elecid.compartmentsFromExpression[ pair ]
@@ -1063,7 +1063,6 @@ rdesigneur.rmoogli.updateMoogliViewer()
self._buildNeuroMesh()
-
self._configureSolvers()
for i in self.adaptorList:
# print(i)
@@ -1326,7 +1325,7 @@ rdesigneur.rmoogli.updateMoogliViewer()
#################################################################
def _configureSolvers( self ) :
- if not hasattr( self, 'chemid' ):
+ if not hasattr( self, 'chemid' ) or len( self.chemDistrib ) == 0:
return
if not hasattr( self, 'dendCompt' ):
raise BuildError( "configureSolvers: no chem meshes defined." )
diff --git a/moose-core/python/rdesigneur/rdesigneurProtos.py b/moose-core/python/rdesigneur/rdesigneurProtos.py
index c85687c5fbe0611b97339e942c274b9f808a8cae..cade79201b388014a2719c513526a0c0eda63417 100644
--- a/moose-core/python/rdesigneur/rdesigneurProtos.py
+++ b/moose-core/python/rdesigneur/rdesigneurProtos.py
@@ -50,6 +50,7 @@ import math
from moose import utils
EREST_ACT = -0.060
+EREST_ACT_HH = -0.070 # A different value is used for the HH squid params
ECA = 0.080
EK = -0.075
SOMA_A = 3.32e-9
@@ -71,7 +72,7 @@ def make_HH_Na(name = 'HH_Na', parent='/library', vmin=-110e-3, vmax=50e-3, vdiv
na.Ek = 50e-3
na.Xpower = 3
na.Ypower = 1
- v = np.linspace(vmin, vmax, vdivs+1) - EREST_ACT
+ v = np.linspace(vmin, vmax, vdivs+1) - EREST_ACT_HH
m_alpha = per_ms * (25 - v * 1e3) / (10 * (np.exp((25 - v * 1e3) / 10) - 1))
m_beta = per_ms * 4 * np.exp(- v * 1e3/ 18)
m_gate = moose.element('%s/gateX' % (na.path))
@@ -100,7 +101,7 @@ def make_HH_K(name = 'HH_K', parent='/library', vmin=-120e-3, vmax=40e-3, vdivs=
k = moose.HHChannel('%s/%s' % (parent, name))
k.Ek = -77e-3
k.Xpower = 4
- v = np.linspace(vmin, vmax, vdivs+1) - EREST_ACT
+ v = np.linspace(vmin, vmax, vdivs+1) - EREST_ACT_HH
n_alpha = per_ms * (10 - v * 1e3)/(100 * (np.exp((10 - v * 1e3)/10) - 1))
n_beta = per_ms * 0.125 * np.exp(- v * 1e3 / 80)
n_gate = moose.element('%s/gateX' % (k.path))
diff --git a/moose-core/tests/python/test_Xchan1.py b/moose-core/tests/python/test_Xchan1.py
index af555663817579d728465bb256055821fa1567a0..d1eb35114cf02a35775b708e43f30dc985db127e 100644
--- a/moose-core/tests/python/test_Xchan1.py
+++ b/moose-core/tests/python/test_Xchan1.py
@@ -63,7 +63,7 @@ def makeModel():
s.concInit = 0.001
chanPool.nInit = 1000.0
# Flux (mM/s) = permeability * N * (conc_out - conc_in )
- chan.permeability = 0.1 * chanPool.volume * 6.022e23 / chanPool.nInit
+ chan.permeability = 0.1 * chanPool.volume * 6.022e23 *0.001 / chanPool.nInit
#####################################################################
fixXreacs.fixXreacs( '/model' )