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Oct 26, 2018
Merged

Channel are written back to genesis and zeroth voxel moose object is … #322

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125 changes: 100 additions & 25 deletions python/moose/genesis/writeKkit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,11 @@
__maintainer__ = "Harsha Rani"
__email__ = "[email protected]"
__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

Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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)
Expand All @@ -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)
Expand Down Expand Up @@ -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"]:
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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()
Expand Down Expand Up @@ -583,7 +653,7 @@ def getColorCheck(color,GENESIS_COLOR_SEQUENCE):
index = color
return index
elif isinstance(color, tuple):
color =[int(x) for x in color[0:3]]
color = map(int, color)[0:3]
index = nearestColorIndex(color, GENESIS_COLOR_SEQUENCE)
return index
elif isinstance(color, int):
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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'
Expand Down Expand Up @@ -741,4 +816,4 @@ def writeFooter2(f):
if written:
print(" file written to ",output)
else:
print(" could be written to kkit format")
print(" could be written to kkit format")