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Merged
merged 3 commits into from
Oct 18, 2018
Merged

CylMesh are written to SBML with annotation field and only zeroth ele… #318

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6f034ec
CylMesh are written to SBML with annotation field and only zeroth ele…
hrani Oct 16, 2018
3d1add2
originaly volex's volume and volex details are populated, but now cyl…
hrani Oct 16, 2018
fdf30c5
Merge branch 'master' into master
dilawar Oct 18, 2018
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65 changes: 46 additions & 19 deletions python/moose/SBML/writeSBML.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,11 @@
**********************************************************************/
/****************************
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
Expand Down Expand Up @@ -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'):
Expand All @@ -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'):
Expand All @@ -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")
Expand All @@ -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):
Expand All @@ -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)
Expand Down Expand Up @@ -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):
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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

Expand All @@ -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

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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) +
Expand All @@ -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)]
Expand All @@ -1011,6 +1035,7 @@ def writeCompt(modelpath, cremodel_):
else:
return False,groupInfo
# write Simulation runtime,simdt,plotdt

def writeSimulationAnnotation(modelpath):
modelAnno = ""
plots = ""
Expand All @@ -1027,15 +1052,16 @@ 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:
q = moose.element(gpath[0])
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:
Expand All @@ -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>"
Expand Down