diff --git a/moose-gui/defaults.py b/moose-gui/defaults.py
index bb49b93c0cb5563f52b064a8e5c6e46bb0aed5ac..6551d2d9eb2cc5ba6d79bf396de8b1d5c81bebfc 100644
--- a/moose-gui/defaults.py
+++ b/moose-gui/defaults.py
@@ -9,6 +9,9 @@ PLOT_FIELDS={
'CaConc':['Ca']
}
FIELD_UNITS={
+ 'volume':'m3',
+ 'Km':'mM',
+ 'kcat':'s-1',
'Vm':'V',
'conc':'mM',
'concInit':'mM',
diff --git a/moose-gui/icons/classIcon/Function.png b/moose-gui/icons/classIcon/Function.png
index cd17659503a400106b3c1e236cccf65ba79cadb8..d516dddb3e6265868ddf7de3fdccc05507ac038a 100644
Binary files a/moose-gui/icons/classIcon/Function.png and b/moose-gui/icons/classIcon/Function.png differ
diff --git a/moose-gui/mload.py b/moose-gui/mload.py
index d495f2c812c558a5988effc3321097a116760b55..916a33c4fa3e392a661cd702606cbed6be926f5a 100644
--- a/moose-gui/mload.py
+++ b/moose-gui/mload.py
@@ -54,6 +54,7 @@ from os.path import basename
from os.path import splitext
from PyQt4 import QtGui, QtCore, Qt
from plugins.setsolver import *
+from moose.SBML import *
def loadGenCsp(target,filename,solver="gsl"):
target = target.replace(" ", "")
@@ -99,7 +100,6 @@ def loadGenCsp(target,filename,solver="gsl"):
return(modelpath1,modelpath1.path)
def loadFile(filename, target, solver="gsl", merge=True):
- print " solver @ loadFile",solver
"""Try to load a model from specified `filename` under the element
`target`.
@@ -187,7 +187,7 @@ def loadFile(filename, target, solver="gsl", merge=True):
if target != '/':
if moose.exists(target):
moose.delete(target)
- model = moose.readSBML(filename,target,'gsl')
+ model = mooseReadSBML(filename,target)
if moose.exists(moose.element(model).path):
moose.Annotator(moose.element(model).path+'/info').modeltype = "sbml"
addSolver(target,'gsl')
diff --git a/moose-gui/objectedit.py b/moose-gui/objectedit.py
index 4e72565e999b1944accdd3a3b9408bf856419945..2545a1e2a562c60ab88cc3cb2a3197ab933d2594 100644
--- a/moose-gui/objectedit.py
+++ b/moose-gui/objectedit.py
@@ -6,9 +6,9 @@
# Maintainer:
# Created: Wed Jun 30 11:18:34 2010 (+0530)
# Version:
-# Last-Updated: Wed Mar 28 14:26:59 2014 (+0530)
+# Last-Updated: Wed Aug 3 15:55:59 2016 (+0530)
# By: Harsha
-# Update #: 917
+# Update #:
# URL:
# Keywords:
# Compatibility:
@@ -206,10 +206,33 @@ class ObjectEditModel(QtCore.QAbstractTableModel):
value = type(oldValue)(value)
ann.setField(field,value)
self.undoStack.append((index,oldValue))
+ elif field == "vector":
+ for ch in ['[',']']:
+ if ch in value:
+ value = value.replace(ch," ")
+ value = value.replace(",", " ")
+ valuelist = []
+ if value.find(',') != -1:
+ valuelist = value.split(",")
+ elif value.find(' ') != -1:
+ valuelist = value.split(" ")
+ else:
+ valuelist = value
+ vectorlist = []
+ for d in valuelist:
+ try:
+ float(d)
+ vectorlist.append(float(d))
+ except:
+ pass
+ from numpy import array
+ a = array( vectorlist )
+ self.mooseObject.setField(field, a)
+
else:
oldValue = self.mooseObject.getField(field)
value = type(oldValue)(value)
- self.mooseObject.setField(field, value)
+ tt = self.mooseObject.setField(field, value)
self.undoStack.append((index, oldValue))
if field == 'name':
self.emit(QtCore.SIGNAL('objectNameChanged(PyQt_PyObject)'), self.mooseObject)
@@ -265,7 +288,7 @@ class ObjectEditModel(QtCore.QAbstractTableModel):
flag |= QtCore.Qt.ItemIsEditable
if isinstance(self.mooseObject, moose.PoolBase) or isinstance(self.mooseObject,moose.Function):
- if field == 'volume':# or field == 'expr':
+ if field == 'volume' or field == 'expr':
pass
elif setter in self.mooseObject.getFieldNames('destFinfo'):
flag |= QtCore.Qt.ItemIsEditable
diff --git a/moose-gui/plugins/default.py b/moose-gui/plugins/default.py
index cb9407270b2c831ef42185e58de0a1d5c27f9a1a..ccf8846d94ebcdd5197672590f7110283a0d9930 100644
--- a/moose-gui/plugins/default.py
+++ b/moose-gui/plugins/default.py
@@ -1204,7 +1204,9 @@ class PlotWidget(QWidget):
x = np.linspace(0, xSrc.currentTime, len(y))
elif isinstance(xSrc, moose.Table):
x = xSrc.vector.copy()
- filename = str(directory)+'/'+'%s.csv' % (ySrc.name)
+ nameVec = ySrc.neighbors['requestOut']
+ name = moose.element(nameVec[0]).name
+ filename = str(directory)+'/'+'%s.csv' %(name)
np.savetxt(filename, np.vstack((x, y)).transpose())
print 'Saved data from %s and %s in %s' % (xSrc.path, ySrc.path, filename)
@@ -1224,7 +1226,7 @@ class PlotWidget(QWidget):
if fileDialog2.exec_():
directory = fileDialog2.directory().path()
for line in self.lineToDataSource.keys():
- self.saveCsv(line,directory)
+ self.saveCsv(line,directory)
def getMenus(self):
diff --git a/moose-gui/plugins/kkit.py b/moose-gui/plugins/kkit.py
index d3706c8b20ecfdfaa0d63addd4f543fb403f0649..a43aea67aa7b0c5984d74f1740a581b90e301136 100644
--- a/moose-gui/plugins/kkit.py
+++ b/moose-gui/plugins/kkit.py
@@ -3,6 +3,7 @@ from PyQt4 import QtGui, QtCore, Qt
from default import *
from moose import *
from moose.genesis import write
+from moose import SBML
#sys.path.append('plugins')
from mplugin import *
from kkitUtil import *
@@ -62,22 +63,54 @@ class KkitPlugin(MoosePlugin):
if filename:
filename = filename
if filters[str(filter_)] == 'SBML':
- writeerror = moose.writeSBML(self.modelRoot,str(filename))
+ self.sceneObj = KkitEditorView(self).getCentralWidget().mooseId_GObj
+ self.coOrdinates = {}
+ for k,v in self.sceneObj.items():
+ if moose.exists(moose.element(k).path+'/info'):
+ annoInfo = Annotator(k.path+'/info')
+ self.coOrdinates[k] = {'x':annoInfo.x, 'y':annoInfo.y}
+
+ #writeerror = moose.writeSBML(self.modelRoot,str(filename),self.coOrdinates)
+ writeerror = -2
+ conisitencyMessages = ""
+ writtentofile = "/test.xml"
+ writeerror,consistencyMessages,writtentofile = moose.SBML.mooseWriteSBML(self.modelRoot,str(filename),self.coOrdinates)
if writeerror == -2:
- QtGui.QMessageBox.warning(None,'Could not save the Model','\n WriteSBML : This copy of MOOSE has not been compiled with SBML writing support.')
+ #QtGui.QMessageBox.warning(None,'Could not save the Model','\n WriteSBML : This copy of MOOSE has not been compiled with SBML writing support.')
+ QtGui.QMessageBox.warning(None,'Could not save the Model',consistencyMessages)
elif writeerror == -1:
QtGui.QMessageBox.warning(None,'Could not save the Model','\n This model is not valid SBML Model, failed in the consistency check')
elif writeerror == 1:
QtGui.QMessageBox.information(None,'Saved the Model','\n File saved to \'{filename}\''.format(filename =filename+'.xml'),QtGui.QMessageBox.Ok)
elif writeerror == 0:
QtGui.QMessageBox.information(None,'Could not save the Model','\nThe filename could not be opened for writing')
+
elif filters[str(filter_)] == 'Genesis':
- self.sceneObj = KkitEditorView(self).getCentralWidget().mooseId_GObj
+ mdtype = moose.Annotator(self.modelRoot+'/info')
self.coOrdinates = {}
+ xycord = []
+ self.sceneObj = KkitEditorView(self).getCentralWidget().mooseId_GObj
+ #Here get x,y coordinates from the Annotation, to save layout position
+ # into genesis
for k,v in self.sceneObj.items():
if moose.exists(moose.element(k).path+'/info'):
annoInfo = Annotator(k.path+'/info')
self.coOrdinates[k] = {'x':annoInfo.x, 'y':annoInfo.y}
+ if mdtype.modeltype != "kkit":
+ #If coordinates come from kkit then directly transfering the co-ordinates
+ # else zoomed in factor is applied before saving it to genesis form
+ for k,v in self.coOrdinates.items():
+ xycord.append(v['x'])
+ xycord.append(v['y'])
+ cmin = min(xycord)
+ cmax = max(xycord)
+ for k,v in self.coOrdinates.items():
+ x = v['x']
+ xprime = int((20*(float(v['x']-cmin)/float(cmax-cmin)))-10)
+ v['x'] = xprime
+ y = v['y']
+ yprime = int((20*(float(v['y']-cmin)/float(cmax-cmin)))-10)
+ v['y'] = -yprime
filename = filename
writeerror = write(self.modelRoot,str(filename),self.coOrdinates)
@@ -309,6 +342,13 @@ class KineticsWidget(EditorWidgetBase):
self.mooseId_GObj = {}
self.srcdesConnection = {}
self.editor = None
+ self.xmin = 0.0
+ self.xmax = 1.0
+ self.ymin = 0.0
+ self.ymax = 1.0
+ self.xratio = 1.0
+ self.yratio = 1.0
+
def reset(self):
self.createdItem = {}
@@ -330,6 +370,7 @@ class KineticsWidget(EditorWidgetBase):
def updateModelView(self):
self.getMooseObj()
+ minmaxratiodict = {'xmin':self.xmin,'xmax':self.xmax,'ymin':self.ymin,'ymax':self.ymax,'xratio':self.xratio,'yratio':self.yratio}
if not self.m:
#At the time of model building
# when we want an empty GraphicView while creating new model,
@@ -337,7 +378,7 @@ class KineticsWidget(EditorWidgetBase):
if hasattr(self, 'view') and isinstance(self.view, QtGui.QWidget):
self.layout().removeWidget(self.view)
#self.sceneContainer.setSceneRect(-self.width()/2,-self.height()/2,self.width(),self.height())
- self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem)
+ self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem,minmaxratiodict)
if isinstance(self,kineticEditorWidget):
self.view.setRefWidget("editorView")
@@ -355,7 +396,7 @@ class KineticsWidget(EditorWidgetBase):
#self.drawLine_arrow()
if hasattr(self, 'view') and isinstance(self.view, QtGui.QWidget):
self.layout().removeWidget(self.view)
- self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem)
+ self.view = GraphicalView(self.modelRoot,self.sceneContainer,self.border,self,self.createdItem,minmaxratiodict)
if isinstance(self,kineticEditorWidget):
#self.getMooseObj()
self.mooseObjOntoscene()
@@ -380,10 +421,10 @@ class KineticsWidget(EditorWidgetBase):
# setupItem
self.m = wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]')
if self.m:
- self.xmin = 0.0
- self.xmax = 1.0
- self.ymin = 0.0
- self.ymax = 1.0
+ # self.xmin = 0.0
+ # self.xmax = 1.0
+ # self.ymin = 0.0
+ # self.ymax = 1.0
self.autoCordinatepos = {}
self.srcdesConnection = {}
@@ -402,6 +443,7 @@ class KineticsWidget(EditorWidgetBase):
self.xmin,self.xmax,self.ymin,self.ymax,self.autoCordinatepos = autoCoordinates(self.meshEntry,self.srcdesConnection)
# TODO: size will be dummy at this point, but size I need the availiable size from the Gui
self.size= QtCore.QSize(1000 ,550)
+
if self.xmax-self.xmin != 0:
self.xratio = (self.size.width()-10)/(self.xmax-self.xmin)
else: self.xratio = self.size.width()-10
@@ -409,8 +451,13 @@ class KineticsWidget(EditorWidgetBase):
if self.ymax-self.ymin:
self.yratio = (self.size.height()-10)/(self.ymax-self.ymin)
else: self.yratio = (self.size.height()-10)
+
self.xratio = int(self.xratio)
self.yratio = int(self.yratio)
+ if self.xratio == 0:
+ self.xratio = 1
+ if self.yratio == 0:
+ self.yratio = 1
def sizeHint(self):
return QtCore.QSize(800,400)
@@ -493,8 +540,13 @@ class KineticsWidget(EditorWidgetBase):
self.mooseId_GObj[element(tabObj.getId())] = tabItem
for funcObj in find_index(memb,'function'):
- funcinfo = moose.element(funcObj.parent).path+'/info'
- funcParent =self.mooseId_GObj[element(funcObj.parent)]
+ funcinfo = moose.element(funcObj).path+'/info'
+ if funcObj.parent.className == "ZombieBufPool" or funcObj.parent.className == "BufPool":
+ funcinfo = moose.element(funcObj).path+'/info'
+ Af = Annotator(funcinfo)
+ funcParent =self.mooseId_GObj[element(funcObj.parent)]
+ elif funcObj.parent.className == "CubeMesh" or funcObj.parent.className == "CylMesh":
+ funcParent = self.qGraCompt[cmpt]
funcItem = FuncItem(funcObj,funcParent)
self.mooseId_GObj[element(funcObj.getId())] = funcItem
self.setupDisplay(funcinfo,funcItem,"Function")
@@ -513,7 +565,6 @@ class KineticsWidget(EditorWidgetBase):
def comptChilrenBoundingRect(self):
for k, v in self.qGraCompt.items():
# compartment's rectangle size is calculated depending on children
- #rectcompt = v.childrenBoundingRect()
rectcompt = calculateChildBoundingRect(v)
v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20))
v.setPen(QtGui.QPen(Qt.QColor(66,66,66,100), self.comptPen, Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin))
@@ -536,9 +587,22 @@ class KineticsWidget(EditorWidgetBase):
bgcolor = getRandColor()
Annoinfo.color = str(bgcolor.name())
if isinstance(self,kineticEditorWidget):
- xpos,ypos = self.positioninfo(info)
+ funct = ["Function","ZombieFunction"]
+ comptt = ["CubeMesh","CylMesh"]
+
+ if objClass in funct:
+ poolt = ["ZombieBufPool","BufPool"]
+ if graphicalObj.mobj.parent.className in poolt:
+ xpos = 0
+ ypos = 30
+ if graphicalObj.mobj.parent.className in comptt:
+ xpos,ypos = self.positioninfo(info)
+ else:
+ xpos,ypos = self.positioninfo(info)
+
self.xylist = [xpos,ypos]
self.xyCord[moose.element(info).parent] = [xpos,ypos]
+
elif isinstance(self,kineticRunWidget):
self.editormooseId_GObj = self.editor.getCentralWidget().mooseId_GObj
editorItem = self.editormooseId_GObj[moose.element(info).parent]
@@ -547,8 +611,8 @@ class KineticsWidget(EditorWidgetBase):
#Annoinfo.x = xpos
#Annoinfo.y = -ypos
graphicalObj.setDisplayProperties(xpos,ypos,textcolor,bgcolor)
- Annoinfo.x = xpos
- Annoinfo.y = ypos
+ #Annoinfo.x = xpos
+ #Annoinfo.y = ypos
def positioninfo(self,iteminfo):
Anno = moose.Annotator(self.modelRoot+'/info')
@@ -572,9 +636,8 @@ class KineticsWidget(EditorWidgetBase):
# ypos = 1.0-(y-self.ymin)*self.yratio
# else:
# ypos = (y-self.ymin)*self.yratio
- ypos = (y-self.ymin)*self.yratio
+ ypos = 1.0 - (y-self.ymin)*self.yratio
xpos = (x-self.xmin)*self.xratio
-
return(xpos,ypos)
def drawLine_arrow(self, itemignoreZooming=False):
@@ -601,7 +664,10 @@ class KineticsWidget(EditorWidgetBase):
self.lineCord(src,des,items,itemignoreZooming)
elif isinstance(out,list):
if len(out) == 0:
- print "Func pool doesn't have sumtotal"
+ if inn.className == "StimulusTable":
+ print inn.name +" doesn't have output"
+ elif inn.className == "ZombieFunction" or inn.className == "Function":
+ print inn.name + " doesn't have sumtotal "
else:
src = self.mooseId_GObj[inn]
for items in (items for items in out ):
@@ -692,7 +758,8 @@ class KineticsWidget(EditorWidgetBase):
l = elePath[0:pos]
linfo = moose.Annotator(l+'/info')
for k, v in self.qGraCompt.items():
- rectcompt = v.childrenBoundingRect()
+ #rectcompt = v.childrenBoundingRect()
+ rectcompt = calculateChildBoundingRect(v)
comptBoundingRect = v.boundingRect()
if not comptBoundingRect.contains(rectcompt):
self.updateCompartmentSize(v)
@@ -709,8 +776,12 @@ class KineticsWidget(EditorWidgetBase):
'''
def updateCompartmentSize(self, compartment):
compartmentBoundary = compartment.rect()
+ #print " compartmentBoundary ",compartmentBoundary, " ",compartment.childrenBoundingRect()
+ #compartmentBoundary =compartment.childrenBoundingRect()
#childrenBoundary = compartment.childrenBoundingRect()
+ #print " 758 ",compartment.childrenBoundaryRect()
childrenBoundary = calculateChildBoundingRect(compartment)
+ #print " ch ",childrenBoundary
x = min(compartmentBoundary.x(), childrenBoundary.x())
y = min(compartmentBoundary.y(), childrenBoundary.y())
width = max(compartmentBoundary.width(), childrenBoundary.width())
@@ -732,9 +803,9 @@ class KineticsWidget(EditorWidgetBase):
# Checking if src (srcdes[0]) or des (srcdes[1]) is ZombieEnz,
# if yes then need to check if cplx is connected to any mooseObject,
# so that when Enzyme is moved, cplx connected arrow to other mooseObject(poolItem) should also be updated
- if( type(srcdes[0]) == EnzItem):
+ if( type(srcdes[0]) == EnzItem or type(srcdes[0] == MMEnzItem)):
self.cplxUpdatearrow(srcdes[0])
- elif( type(srcdes[1]) == EnzItem):
+ elif( type(srcdes[1]) == EnzItem or type(srcdes[1] == MMEnzItem)):
self.cplxUpdatearrow(srcdes[1])
# For calcArrow(src,des,endtype,itemignoreZooming) is to be provided
arrow = calcArrow(srcdes,self.itemignoreZooming,self.iconScale)
diff --git a/moose-gui/plugins/kkitOrdinateUtil.py b/moose-gui/plugins/kkitOrdinateUtil.py
index 36e8e833251bfbaaab70b2ad06264d98ad15f918..01bcafd40975b80a454b73ba7992ae86b2979724 100644
--- a/moose-gui/plugins/kkitOrdinateUtil.py
+++ b/moose-gui/plugins/kkitOrdinateUtil.py
@@ -76,6 +76,7 @@ def setupMeshObj(modelRoot):
def sizeHint(self):
return QtCore.QSize(800,400)
+
def getxyCord(xcord,ycord,list1):
for item in list1:
# if isinstance(item,Function):
@@ -175,8 +176,6 @@ def countitems(mitems,objtype):
return(uniqItems,countuniqItems)
def autoCoordinates(meshEntry,srcdesConnection):
- #for cmpt,memb in meshEntry.items():
- # print memb
xmin = 0.0
xmax = 1.0
ymin = 0.0
@@ -184,15 +183,19 @@ def autoCoordinates(meshEntry,srcdesConnection):
G = nx.Graph()
for cmpt,memb in meshEntry.items():
for enzObj in find_index(memb,'enzyme'):
- G.add_node(enzObj.path)
+ #G.add_node(enzObj.path)
+ G.add_node(enzObj.path,label='',shape='ellipse',color='',style='filled',fontname='Helvetica',fontsize=12,fontcolor='blue')
for cmpt,memb in meshEntry.items():
for poolObj in find_index(memb,'pool'):
- G.add_node(poolObj.path)
+ #G.add_node(poolObj.path)
+ G.add_node(poolObj.path,label = poolObj.name,shape = 'box',color = '',style = 'filled',fontname = 'Helvetica',fontsize = 12,fontcolor = 'blue')
for cplxObj in find_index(memb,'cplx'):
G.add_node(cplxObj.path)
- G.add_edge((cplxObj.parent).path,cplxObj.path)
+ G.add_node(cplxObj.path,label = cplxObj.name,shape = 'box',color = '',style = 'filled',fontname = 'Helvetica',fontsize = 12,fontcolor = 'blue')
+ #G.add_edge((cplxObj.parent).path,cplxObj.path)
for reaObj in find_index(memb,'reaction'):
- G.add_node(reaObj.path)
+ #G.add_node(reaObj.path)
+ G.add_node(reaObj.path,label='',shape='circle',color='')
for inn,out in srcdesConnection.items():
if (inn.className =='ZombieReac'): arrowcolor = 'green'
@@ -216,11 +219,16 @@ def autoCoordinates(meshEntry,srcdesConnection):
for items in (items for items in out ):
G.add_edge(element(items[0]).path,inn.path)
- nx.draw(G,pos=nx.spring_layout(G))
- #plt.savefig('/home/harsha/Desktop/netwrokXtest.png')
+ #nx.draw(G,pos=nx.spring_layout(G))
+ #position = nx.spring_layout(G)
+ #import matplotlib.pyplot as plt
+ #plt.savefig('/home/harsha/Trash/Trash_SBML/test.png')
+ position = nx.graphviz_layout(G, prog = 'dot')
+ #agraph = nx.to_agraph(G)
+ #agraph.draw("test.png", format = 'png', prog = 'dot')
xcord = []
ycord = []
- position = nx.spring_layout(G)
+
for item in position.items():
xy = item[1]
ann = moose.Annotator(item[0]+'/info')
@@ -228,9 +236,7 @@ def autoCoordinates(meshEntry,srcdesConnection):
xcord.append(xy[0])
ann.y = xy[1]
ycord.append(xy[1])
- # for y in position.values():
- # xcord.append(y[0])
- # ycord.append(y[1])
+
if xcord and ycord:
xmin = min(xcord)
xmax = max(xcord)
diff --git a/moose-gui/plugins/kkitQGraphics.py b/moose-gui/plugins/kkitQGraphics.py
index 222a07d4764ed16b4b9541e88e5f0b42133d0762..27ddbe3555d0bff5f9672ba9db5dd2b15b3dc7c6 100644
--- a/moose-gui/plugins/kkitQGraphics.py
+++ b/moose-gui/plugins/kkitQGraphics.py
@@ -60,7 +60,7 @@ class FuncItem(KineticsDisplayItem):
fontMetrics = QtGui.QFontMetrics(font)
def __init__(self, mobj, parent):
super(FuncItem, self).__init__(mobj, parent)
- self.setFlag(QtGui.QGraphicsItem.ItemIsMovable, False)
+ self.setFlag(QtGui.QGraphicsItem.ItemIsMovable, True)
self.funcImage = QImage('icons/classIcon/Function.png').scaled(15,33)
self.bg = QtGui.QGraphicsRectItem(self)
self.bg.setAcceptHoverEvents(True)
@@ -75,8 +75,14 @@ class FuncItem(KineticsDisplayItem):
def setDisplayProperties(self,x,y,textcolor,bgcolor):
"""Set the display properties of this item."""
- #With Respect to BuffPool (parent) I am placing at 0,30 (which is below the BuffPool)
- self.setGeometry(0, 30,self.gobj.boundingRect().width(),self.gobj.boundingRect().height())
+ #With Respect to BuffPool (as parent which is in old genesis) then function are placed at 0,30 (which is below the BuffPool)
+ #else if droped from the GUI then placed wrt position
+ #self.setGeometry(0, 30,self.gobj.boundingRect().width(),self.gobj.boundingRect().height())
+ #self.setGeometry(x,y)
+ if self.gobj.mobj.parent.className == "ZombieBufPool" or self.gobj.mobj.parent.className == "BufPool":
+ self.setGeometry(0, 30,self.gobj.boundingRect().width(),self.gobj.boundingRect().height())
+ else:
+ self.setGeometry(x,y,self.gobj.boundingRect().width(),self.gobj.boundingRect().height())
self.bg.setBrush(QtGui.QBrush(bgcolor))
self.setFlag(QtGui.QGraphicsItem.ItemIsMovable,False)
def refresh(self,scale):
@@ -126,7 +132,7 @@ class PoolItem(KineticsDisplayItem):
"""Class for displaying pools. Uses a QGraphicsSimpleTextItem to
display the name."""
#fontMetrics = None
- font =QtGui.QFont(KineticsDisplayItem.defaultFontName)
+ font = QtGui.QFont(KineticsDisplayItem.defaultFontName)
font.setPointSize(KineticsDisplayItem.defaultFontSize)
fontMetrics = QtGui.QFontMetrics(font)
def __init__(self, mobj, parent):
diff --git a/moose-gui/plugins/kkitUtil.py b/moose-gui/plugins/kkitUtil.py
index 5efc02c277e040a7e12c6cc434ad3ce0825baf5c..a83a496c320e9e9ddb578e8e4665ad60036c5e73 100644
--- a/moose-gui/plugins/kkitUtil.py
+++ b/moose-gui/plugins/kkitUtil.py
@@ -13,7 +13,7 @@ colormap_file = open(os.path.join(config.settings[config.KEY_COLORMAP_DIR], 'rai
colorMap = pickle.load(colormap_file)
colormap_file.close()
-ignoreColor= ["mistyrose","antiquewhite","aliceblue","azure","bisque","black","blanchedalmond","blue","cornsilk","darkolivegreen","darkslategray","dimgray","floralwhite","gainsboro","ghostwhite","honeydew","ivory","lavender","lavenderblush","lemonchiffon","lightcyan","lightgoldenrodyellow","lightgray","lightyellow","linen","mediumblue","mintcream","navy","oldlace","papayawhip","saddlebrown","seashell","snow","wheat","white","whitesmoke"]
+ignoreColor= ["mistyrose","antiquewhite","aliceblue","azure","bisque","black","blanchedalmond","blue","cornsilk","darkolivegreen","darkslategray","dimgray","floralwhite","gainsboro","ghostwhite","honeydew","ivory","lavender","lavenderblush","lemonchiffon","lightcyan","lightgoldenrodyellow","lightgray","lightyellow","linen","mediumblue","mintcream","navy","oldlace","papayawhip","saddlebrown","seashell","snow","wheat","white","whitesmoke","aquamarine","lightsalmon","moccasin","limegreen","snow","sienna","beige","dimgrey","lightsage"]
matplotcolor = {}
for name,hexno in matplotlib.colors.cnames.iteritems():
matplotcolor[name]=hexno
@@ -56,6 +56,8 @@ def colorCheck(fc_bgcolor,fcbg):
if string its taken as colorname further down in validColorcheck checked for valid color, \
but for tuple and list its taken as r,g,b value.
"""
+ #import re
+ #fc_bgcolor = re.sub('[^a-zA-Z0-9-_*.]', '', fc_bgcolor)
if isinstance(fc_bgcolor,str):
if fc_bgcolor.startswith("#"):
fc_bgcolor = QColor(fc_bgcolor)
@@ -138,14 +140,13 @@ def calculateChildBoundingRect(compt):
''' All the children including pool,reac,enz,polygon(arrow),table '''
if not isinstance(l,QtSvg.QGraphicsSvgItem):
- xpos.append((l.pos().x())+(l.boundingRect().bottomRight().x()))
- xpos.append(l.pos().x())
- ypos.append(l.pos().y()+l.boundingRect().bottomRight().y())
- ypos.append(l.pos().y())
-
+ if (not isinstance(l,QtGui.QGraphicsPolygonItem)):
+ xpos.append((l.pos().x())+(l.boundingRect().bottomRight().x()))
+ xpos.append(l.pos().x())
+ ypos.append(l.pos().y()+l.boundingRect().bottomRight().y())
+ ypos.append(l.pos().y())
if (isinstance(l,PoolItem) or isinstance(l,EnzItem)):
''' For Enz cplx height and for pool function height needs to be taken'''
-
for ll in l.childItems():
''' eleminating polygonItem (arrow) [This is happen in cross-compartment model that arrow from one compartment will be child]
pool's outboundary RectItem and Enz's outerboundary Ellipse is eleminating since its same
@@ -160,4 +161,4 @@ def calculateChildBoundingRect(compt):
else:
calculateRectcompt = compt.rect()
- return calculateRectcompt
\ No newline at end of file
+ return calculateRectcompt
diff --git a/moose-gui/plugins/kkitViewcontrol.py b/moose-gui/plugins/kkitViewcontrol.py
index 91bcef43751fdd3d679e88ba935b0cc999514d29..c5c74b54c770e7d01ce640f4796a6821f633fa51 100644
--- a/moose-gui/plugins/kkitViewcontrol.py
+++ b/moose-gui/plugins/kkitViewcontrol.py
@@ -10,8 +10,9 @@ from moose import utils
class GraphicalView(QtGui.QGraphicsView):
- def __init__(self, modelRoot,parent,border,layoutPt,createdItem):
+ def __init__(self, modelRoot,parent,border,layoutPt,createdItem,minmaxratio):
QtGui.QGraphicsView.__init__(self,parent)
+ self.minmaxratioDict = minmaxratio
self.state = None
self.move = False
self.resetState()
@@ -136,7 +137,6 @@ class GraphicalView(QtGui.QGraphicsView):
def editorMouseMoveEvent(self, event):
-
if self.state["press"]["mode"] == INVALID:
self.state["move"]["happened"] = False
return
@@ -148,7 +148,7 @@ class GraphicalView(QtGui.QGraphicsView):
for item in self.selectedItems:
if isinstance(item, KineticsDisplayItem) and not isinstance(item,ComptItem) and not isinstance(item,CplxItem):
item.moveBy(displacement.x(), displacement.y())
- self.layoutPt.positionChange(item.mobj.path)
+ self.layoutPt.positionChange(item.mobj.path)
self.state["press"]["pos"] = event.pos()
return
@@ -161,7 +161,8 @@ class GraphicalView(QtGui.QGraphicsView):
actionType = str(item.data(0).toString())
if actionType == "move":
QtGui.QApplication.setOverrideCursor(QtGui.QCursor(QtCore.Qt.CrossCursor))
- initial = item.parent().pos()
+ initial = self.mapToScene(self.state["press"]["pos"])
+ #initial = item.parent().pos()
final = self.mapToScene(event.pos())
displacement = final-initial
if isinstance(item.parent(),KineticsDisplayItem):
@@ -169,10 +170,18 @@ class GraphicalView(QtGui.QGraphicsView):
if moose.exists(itemPath):
iInfo = itemPath+'/info'
anno = moose.Annotator(iInfo)
- anno.x = self.mapToScene(event.pos()).x()
- anno.y = self.mapToScene(event.pos()).y()
+ modelAnno = moose.Annotator(self.modelRoot+'/info')
+ if modelAnno.modeltype == "kkit":
+ x = ((self.mapToScene(event.pos()).x())+(self.minmaxratioDict['xmin']*self.minmaxratioDict['xratio']))/self.minmaxratioDict['xratio']
+ y = (1.0 - self.mapToScene(event.pos()).y()+(self.minmaxratioDict['ymin']*self.minmaxratioDict['yratio']))/self.minmaxratioDict['yratio']
+ anno.x = x
+ anno.y = y
+ elif(modelAnno.modeltype == "new_kkit" or modelAnno.modeltype == "sbml" or modelAnno.modeltype == "cspace"):
+ anno.x = self.mapToScene(event.pos()).x()
+ anno.y = self.mapToScene(event.pos()).y()
- if not isinstance(item.parent(),FuncItem) and not isinstance(item.parent(),CplxItem):
+ #if not isinstance(item.parent(),FuncItem) and not isinstance(item.parent(),CplxItem):
+ if not isinstance(item.parent(),CplxItem):
self.removeConnector()
item.parent().moveBy(displacement.x(), displacement.y())
if isinstance(item.parent(),PoolItem):
@@ -241,8 +250,9 @@ class GraphicalView(QtGui.QGraphicsView):
def editorMouseReleaseEvent(self, event):
if self.move:
- #self.move = False
+ self.move = False
self.setCursor(Qt.Qt.ArrowCursor)
+
if self.state["press"]["mode"] == INVALID:
self.state["release"]["mode"] = INVALID
self.resetState()
@@ -410,7 +420,6 @@ class GraphicalView(QtGui.QGraphicsView):
startingPosition = self.state["press"]["pos"]
endingPosition = event.pos()
displacement = endingPosition - startingPosition
-
x0 = startingPosition.x()
x1 = endingPosition.x()
y0 = startingPosition.y()
@@ -531,6 +540,7 @@ class GraphicalView(QtGui.QGraphicsView):
self.xDisp = 0
self.yDisp = 0
self.connectionSign = None
+
if isinstance(item.mobj,PoolBase) or isinstance(item.mobj,ReacBase):
if l == "clone":
self.connectionSign = QtSvg.QGraphicsSvgItem('icons/clone.svg')
@@ -545,6 +555,7 @@ class GraphicalView(QtGui.QGraphicsView):
self.connectionSign.setZValue(1)
self.connectionSign.setToolTip("Click and drag to clone the object")
self.connectorlist["clone"] = self.connectionSign
+
if isinstance(item.mobj,PoolBase):
if l == "plot":
self.connectionSign = QtSvg.QGraphicsSvgItem('icons/plot.svg')
@@ -561,29 +572,45 @@ class GraphicalView(QtGui.QGraphicsView):
self.connectorlist["plot"] = self.connectionSign
if l == "move":
- self.connectionSign = QtSvg.QGraphicsSvgItem('icons/move.svg')
- self.connectionSign.setData(0, QtCore.QVariant("move"))
- self.connectionSign.setParent(self.connectionSource)
- self.connectionSign.setToolTip("Drag to move.")
- self.connectionSign.setScale(
- (1.0 * rectangle.height()) / self.connectionSign.boundingRect().height()
- )
- position = item.mapToParent(rectangle.topLeft())
- self.xDisp = 15
- self.yDisp = 2
- self.connectionSign.setZValue(1)
- self.connectorlist["move"] = self.connectionSign
+ if ((item.mobj.parent.className == "ZombieEnz") or (item.mobj.parent.className == "Enz")):
+ pass
+ else:
+ self.connectionSign = QtSvg.QGraphicsSvgItem('icons/move.svg')
+ self.connectionSign.setData(0, QtCore.QVariant("move"))
+ self.connectionSign.setParent(self.connectionSource)
+ self.connectionSign.setToolTip("Drag to move.")
+ if ( item.mobj.className == "ZombieFunction" or item.mobj.className == "Function"):
+ self.connectionSign.setScale(
+ (0.75 * rectangle.height()) / self.connectionSign.boundingRect().height()
+ )
+ else:
+ self.connectionSign.setScale(
+ (1 * rectangle.height()) / self.connectionSign.boundingRect().height()
+ )
+ position = item.mapToParent(rectangle.topLeft())
+ self.xDisp = 15
+ self.yDisp = 2
+ self.connectionSign.setZValue(1)
+ self.connectorlist["move"] = self.connectionSign
elif l == "delete":
- self.connectionSign = QtSvg.QGraphicsSvgItem('icons/delete.svg')
- self.connectionSign.setParent(self.connectionSource)
- self.connectionSign.setData(0, QtCore.QVariant("delete"))
- self.connectionSign.setScale(
- (1.0 * rectangle.height()) / self.connectionSign.boundingRect().height()
- )
- position = item.mapToParent(rectangle.topRight())
- self.connectionSign.setZValue(1)
- self.connectionSign.setToolTip("Delete the object")
- self.connectorlist["delete"] = self.connectionSign
+ if ((item.mobj.parent.className == "ZombieEnz") or (item.mobj.parent.className == "Enz")):
+ pass
+ else:
+ self.connectionSign = QtSvg.QGraphicsSvgItem('icons/delete.svg')
+ self.connectionSign.setParent(self.connectionSource)
+ self.connectionSign.setData(0, QtCore.QVariant("delete"))
+ if ( item.mobj.className == "ZombieFunction" or item.mobj.className == "Function"):
+ self.connectionSign.setScale(
+ (0.75 * rectangle.height()) / self.connectionSign.boundingRect().height()
+ )
+ else:
+ self.connectionSign.setScale(
+ (1.0 * rectangle.height()) / self.connectionSign.boundingRect().height()
+ )
+ position = item.mapToParent(rectangle.topRight())
+ self.connectionSign.setZValue(1)
+ self.connectionSign.setToolTip("Delete the object")
+ self.connectorlist["delete"] = self.connectionSign
if self.connectionSign != None:
self.connectionSign.setFlag(QtGui.QGraphicsItem.ItemIsSelectable,True)
@@ -1096,16 +1123,34 @@ class GraphicalView(QtGui.QGraphicsView):
des.expr = expr
moose.connect( src, 'nOut', des.x[numVariables], 'input' )
- elif ( isinstance(moose.element(src),Function) and (moose.element(des).className=="Pool") ):
+ elif ( isinstance(moose.element(src),Function) and (moose.element(des).className=="Pool") or
+ isinstance(moose.element(src),ZombieFunction) and (moose.element(des).className=="ZombiePool")
+ ):
if ((element(des).parent).className != 'Enz'):
- moose.connect(src, 'valueOut', des, 'increment', 'OneToOne')
+ #moose.connect(src, 'valueOut', des, 'increment', 'OneToOne')
+ found = False
+ if len(moose.element(src).neighbors["valueOut"]):
+ for psl in moose.element(src).neighbors["valueOut"]:
+ if moose.element(psl) == moose.element(des):
+ found = True
+ if found == False:
+ moose.connect(src, 'valueOut', des, 'setN', 'OneToOne')
+ else:
+ srcdesString = '\"'+moose.element(src).name+'\" is already connected to \"'+ moose.element(des).name +'\" \n'
+ QtGui.QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok)
+
+
else:
srcdesString = element(src).className+'-- EnzCplx'
QtGui.QMessageBox.information(None,'Connection Not possible','\'{srcdesString}\' not allowed to connect'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok)
callsetupItem = False
- elif ( isinstance(moose.element(src),Function) and (moose.element(des).className=="BufPool") ):
+ elif ( isinstance(moose.element(src),Function) and (moose.element(des).className=="BufPool") or
+ isinstance(moose.element(src),ZombieFunction) and (moose.element(des).className=="ZombieBufPool")
+ ):
moose.connect(src, 'valueOut', des, 'setN', 'OneToOne')
- elif ( isinstance(moose.element(src),Function) and (isinstance(moose.element(des),ReacBase) ) ):
+ elif ( isinstance(moose.element(src),Function) and (isinstance(moose.element(des),ReacBase) ) or
+ isinstance(moose.element(src),ZombieFunction) and (moose.element(des).className=="ZombieReac")
+ ):
moose.connect(src, 'valueOut', des, 'setNumKf', 'OneToOne')
elif (((isinstance(moose.element(src),ReacBase))or (isinstance(moose.element(src),EnzBase))) and (isinstance(moose.element(des),PoolBase))):
found = False
diff --git a/moose-gui/plugins/modelBuild.py b/moose-gui/plugins/modelBuild.py
index 751b7c76bfcb1831d45a80630c6f70a2584a7031..471d8e9eaf63953343cb3a7e968e5e2135e27860 100644
--- a/moose-gui/plugins/modelBuild.py
+++ b/moose-gui/plugins/modelBuild.py
@@ -25,13 +25,16 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
# modelRoot = modelpath[0:modelpath.find('/',1)]
# else:
# modelRoot = modelpath
+ print "28 ",modelpath
if moose.exists(modelpath+'/info'):
mType = moose.Annotator((moose.element(modelpath+'/info'))).modeltype
-
+ print " 1 event_pos ",event_pos
itemAtView = view.sceneContainerPt.itemAt(view.mapToScene(event_pos))
+ print "2 ",itemAtView
pos = view.mapToScene(event_pos)
+ print " 3 ",pos
modelpath = moose.element(modelpath)
-
+ print " model path @34 ",modelpath
if num:
string_num = ret_string+str(num)
else:
@@ -121,11 +124,17 @@ def checkCreate(scene,view,modelpath,mobj,string,ret_string,num,event_pos,layout
updateCompartmentSize(compt)
elif string == "Function":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
-
funcObj = moose.Function(mobj.path+'/'+string_num)
funcinfo = moose.Annotator(funcObj.path+'/info')
- moose.connect( funcObj, 'valueOut', mobj ,'setN' )
- funcParent = layoutPt.mooseId_GObj[element(mobj.path)]
+ #moose.connect( funcObj, 'valueOut', mobj ,'setN' )
+ poolclass = ["ZombieBufPool","BufPool"]
+ comptclass = ["CubeMesh","cyclMesh"]
+ if mobj.className in poolclass:
+ funcParent = layoutPt.mooseId_GObj[element(mobj.path)]
+ elif mobj.className in comptclass:
+ funcParent = layoutPt.qGraCompt[moose.element(mobj)]
+ posWrtComp = funcParent.mapFromScene(pos).toPoint()
+ #posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
qGItem = FuncItem(funcObj,funcParent)
#print " function ", posWrtComp.x(),posWrtComp.y()
qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),QtGui.QColor('red'),QtGui.QColor('green'))
@@ -222,7 +231,6 @@ def createObj(scene,view,modelpath,string,pos,layoutPt):
mobj = itemAtView.parent().mobj
else:
mobj = itemAtView.mobj
-
if string == "CubeMesh" or string == "CylMesh":
ret_string,num = findUniqId(moose.element(modelpath),"Compartment",0)
comptexist = moose.wildcardFind(modelpath+'/##[ISA=ChemCompt]')
@@ -245,6 +253,9 @@ def createObj(scene,view,modelpath,string,pos,layoutPt):
ret_string,num = findUniqId(mobj,string,num)
elif string == "Function":
+ mobj = findCompartment(mobj)
+ ret_string,num = findUniqId(mobj,string,num)
+ '''
if itemAt != None:
if ((mobj).className != "BufPool"):
QtGui.QMessageBox.information(None,'Drop Not possible','\'{newString}\' has to have BufPool as its parent'.format(newString =string),QtGui.QMessageBox.Ok)
@@ -254,7 +265,7 @@ def createObj(scene,view,modelpath,string,pos,layoutPt):
else:
QtGui.QMessageBox.information(None,'Drop Not possible','\'{newString}\' has to have BufPool as its parent'.format(newString =string),QtGui.QMessageBox.Ok)
return
-
+ '''
elif string == "Enz" or string == "MMenz":
if itemAt != None:
if ((mobj).className != "Pool" and (mobj).className != "BufPool"):
diff --git a/moose-gui/plugins/setsolver.py b/moose-gui/plugins/setsolver.py
index ae6fb418d053a7de93f02281bbeadedcf6e1c7f6..f55b0673f6b90faa36d398931030e15fef4041fa 100644
--- a/moose-gui/plugins/setsolver.py
+++ b/moose-gui/plugins/setsolver.py
@@ -46,9 +46,32 @@ def addSolver(modelRoot,solver):
setCompartmentSolver(modelRoot,currentSolver)
return True
return False
-
+
+def positionCompt( compt, side, shiftUp ):
+ y0 = compt.y0
+ y1 = compt.y1
+ if ( shiftUp ):
+ compt.y0 = (y0 + side)
+ compt.y1 = (y1 + side)
+ else:
+ compt.y0 = (y0 - y1 )
+ compt.y1 = 0
+
def setCompartmentSolver(modelRoot,solver):
compts = moose.wildcardFind(modelRoot+'/##[ISA=ChemCompt]')
+
+ if ( len(compts) > 3 ):
+ print "Warning: setSolverOnCompt Cannot handle " ,
+ len(compts) , " chemical compartments\n"
+ return;
+
+ if ( len(compts) == 2 ):
+ positionCompt( compts[0], compts[1].dy, True )
+
+ if ( len(compts) == 3 ):
+ positionCompt( compts[0], compts[1].dy, True )
+ positionCompt( compts[2], compts[1].dy, False )
+
for compt in compts:
if ( solver == 'gsl' ) or (solver == 'Runge Kutta'):
ksolve = moose.Ksolve( compt.path+'/ksolve' )
@@ -60,15 +83,15 @@ def setCompartmentSolver(modelRoot,solver):
stoich.ksolve = ksolve
if moose.exists(compt.path):
stoich.path = compt.path+"/##"
+
stoichList = moose.wildcardFind(modelRoot+'/##[ISA=Stoich]')
+
if len( stoichList ) == 2:
stoichList[1].buildXreacs( stoichList[0] )
+
if len( stoichList ) == 3:
stoichList[1].buildXreacs (stoichList [0])
stoichList[1].buildXreacs (stoichList [2])
for i in stoichList:
- i.filterXreacs()
-
- for x in moose.wildcardFind( modelRoot+'/data/graph#/#' ):
- x.tick = 18
\ No newline at end of file
+ i.filterXreacs()
\ No newline at end of file