Skip to content

Commit

Permalink
CylMesh,EndoMesh,NeuroMesh compartment are written to SBML as compart…
Browse files Browse the repository at this point in the history 
…ment with annotation field in which surround,isMembraneBound,numDiffCompts
  • Loading branch information
@hrani
hrani committed Nov 7, 2018
1 parent e5868be commit 740a7a6
Show file tree
Hide file tree
Showing 2 changed files with 82 additions and 38 deletions.
116 changes: 80 additions & 36 deletions python/moose/SBML/writeSBML.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,15 @@
** copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
Created : Friday May 27 12:19:00 2016(+0530)
Version
Last-Updated: Mon 30 Apr 15:10:00 2018(+0530)
Last-Updated: Thr 08 Nov 00:15:10 2018(+0530)
By: HarshaRani
**********************************************************************/
/****************************
2018
Nov 06: All the Mesh Cyl,Cube,Neuro,Endo Mesh's can be written into SBML format with annotation field where Meshtype\
numDiffCompts,isMembraneBound and surround are written out.
For EndoMesh check made to see surround is specified
Oct 20: EndoMesh added to SBML
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
Expand Down Expand Up @@ -108,6 +112,7 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
neutralNotes = ""

specieslist = moose.wildcardFind(modelpath + '/##[0][ISA=PoolBase]')

if specieslist:
neutralPath = getGroupinfo(specieslist[0])
if moose.exists(neutralPath.path + '/info'):
Expand All @@ -124,11 +129,12 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
writeUnits(cremodel_)

modelAnno = writeSimulationAnnotation(modelpath)

if modelAnno:
cremodel_.setAnnotation(modelAnno)
groupInfo = {}

compartexist, groupInfo = writeCompt(modelpath, cremodel_)
compterrors =""
compartexist, groupInfo,compterrors = writeCompt(modelpath, cremodel_)

if compartexist == True:
species = writeSpecies( modelpath,cremodel_,sbmlDoc,sceneitems,groupInfo)
Expand Down Expand Up @@ -170,13 +176,16 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
writeTofile = filepath + "/" + filename + '.xml'
writeSBMLToFile(sbmlDoc, writeTofile)
return True, consistencyMessages, writeTofile

if (not SBMLok):
#cerr << "Errors encountered " << endl
consistencyMessages = "Errors encountered"
return -1, consistencyMessages
else:
return False, "Atleast one compartment should exist to write SBML"
if compterrors:
return False, compterrors
else:
return False,"Atleast one compartment should exist to write SBML"

def writeEnz(modelpath, cremodel_, sceneitems,groupInfo):
for enz in moose.wildcardFind(modelpath + '/##[0][ISA=EnzBase]'):
Expand Down Expand Up @@ -991,49 +1000,81 @@ def writeCompt(modelpath, cremodel_):
# getting all the compartments
compts = moose.wildcardFind(modelpath + '/##[0][ISA=ChemCompt]')
groupInfo = {}
comptID_sbml = {}
for compt in compts:
comptAnno = ""
comptName = convertSpecialChar(compt.name)
# converting m3 to litre
if isinstance(compt,moose.CylMesh):
createCompt = True
size = compt.volume * pow(10, 3)
ndim = compt.numDimensions
csetId = (str(idBeginWith(comptName +
"_" +
str(compt.getId().value) +
"_" +
str(compt.getDataIndex()) +
"_")))
comptID_sbml[compt] = (csetId)
if isinstance(compt,moose.EndoMesh):
if comptID_sbml.get(compt.surround) == None:
createCompt = False
return False,groupInfo,"Outer compartment need to be specified for EndoMesh "
#return " EndoMesh need to outer compartment to be specified "
else:
c1.outside = comptID_sbml[compt.surround]
comptAnno = "<moose:CompartmentAnnotation><moose:Mesh>" + \
str(compt.className) + "</moose:Mesh>\n" + \
"<moose:surround>" + \
str(comptID_sbml[compt.surround])+ "</moose:surround>\n" + \
"<moose:isMembraneBound>" + \
str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n" + \
"</moose:CompartmentAnnotation>"
elif isinstance(compt,moose.NeuroMesh) or 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:isMembraneBound>" + \
str(compt.isMembraneBound)+ "</moose:isMembraneBound>\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) +
"_" +
str(compt.getDataIndex()) +
"_")))
c1.setName(comptName)
c1.setConstant(True)
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+'/##[0][TYPE=Neutral]'):
grp_cmpt = findGroup_compt(grp.parent)
try:
value = groupInfo[moose.element(grp)]
except KeyError:
# Grp is not present
groupInfo[moose.element(grp)] = []

else:
comptAnno = "<moose:CompartmentAnnotation><moose:Mesh>" + \
str(compt.className) + "</moose:Mesh>\n" + \
"<moose:isMembraneBound>" + \
str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n" + \
"</moose:CompartmentAnnotation>"
if createCompt:
c1 = cremodel_.createCompartment()
c1.setId(csetId)
c1.setName(comptName)
c1.setConstant(True)
c1.setSize(compt.volume*pow(10,3))
#c1.setSize(size)
if comptAnno:
c1.setAnnotation(comptAnno)
c1.setSpatialDimensions(ndim)
if ndim == 3:
c1.setUnits('volume')
elif ndim == 2:
c1.setUnits('area')
elif ndim == 1:
c1.setUnits('metre')

#For each compartment get groups information along
for grp in moose.wildcardFind(compt.path+'/##[0][TYPE=Neutral]'):
grp_cmpt = findGroup_compt(grp.parent)
try:
value = groupInfo[moose.element(grp)]
except KeyError:
# Grp is not present
groupInfo[moose.element(grp)] = []


if compts:
return True,groupInfo
return True,groupInfo,""
else:
return False,groupInfo
return False,groupInfo,""
# write Simulation runtime,simdt,plotdt

def writeSimulationAnnotation(modelpath):
Expand Down Expand Up @@ -1061,7 +1102,9 @@ def writeSimulationAnnotation(modelpath):
ori = q.path
name = convertSpecialChar(q.name)
graphSpefound = False
while not(isinstance(moose.element(q), moose.CubeMesh) or isinstance(moose.element(q),moose.CylMesh)):

while not(isinstance(moose.element(q), moose.CubeMesh) or isinstance(moose.element(q),moose.CylMesh) \
or isinstance(moose.element(q), moose.EndoMesh) or isinstance(moose.element(q),moose.NeuroMesh)):
q = q.parent
graphSpefound = True
if graphSpefound:
Expand All @@ -1076,6 +1119,7 @@ def writeSimulationAnnotation(modelpath):
if plots != " ":
modelAnno = modelAnno + "<moose:plots> " + plots + "</moose:plots>\n"
modelAnno = modelAnno + "</moose:ModelAnnotation>"

return modelAnno

def recalculatecoordinates(modelpath, mObjlist,xcord,ycord):
Expand Down
4 changes: 2 additions & 2 deletions python/moose/chemUtil/chemConnectUtil.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
__maintainer__ = "Harsha Rani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
__updated__ = "Aug 8 2017"
__updated__ = "Nov 8 2018"

import moose
import numpy as np
Expand Down Expand Up @@ -193,7 +193,7 @@ def countitems(mitems,objtype):
def findCompartment(element):
if element.path == '/':
return moose.element('/')
elif mooseIsInstance(element, ["CubeMesh", "CylMesh"]):
elif mooseIsInstance(element, ["CubeMesh", "CylMesh","EndoMesh","NeuroMesh"]):
return (element)
else:
return findCompartment(moose.element(element.parent))
Expand Down

0 comments on commit 740a7a6

Please sign in to comment.