moose-gui/plugins/buildkkit.py at master · BhallaLab/moose-gui · GitHub

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import sys

import os

import math

import re

from PyQt4 import QtGui, QtCore, Qt

#import pygraphviz as pgv

import networkx as nx

#sys.path.insert(0, '/home/harsha/BuildQ/gui')

import numpy as np

import config

import pickle

from default import *

from moose import *

sys.path.append('plugins')

from mplugin import *

from kkitUtil import *

from kkitQGraphics import PoolItem, ReacItem,EnzItem,CplxItem,ComptItem

from kkitViewcontrol import *

from kkitCalcArrow import *

from kkitOrdinateUtil import *

import posixpath

from mtoolbutton import MToolButton

class KkitPlugin(MoosePlugin):

"""Default plugin for MOOSE GUI"""

def __init__(self, *args):

#print args

MoosePlugin.__init__(self, *args)

def getPreviousPlugin(self):

return None

def getNextPlugin(self):

return None

def getAdjacentPlugins(self):

return []

def getViews(self):

return self._views

def getCurrentView(self):

return self.currentView

def getEditorView(self):

if not hasattr(self, 'editorView'):

self.editorView = KkitEditorView(self)

self.editorView.getCentralWidget().editObject.connect(self.mainWindow.objectEditSlot)

self.currentView = self.editorView

return self.editorView

def getRunView(self):

view = MoosePlugin.getRunView(self)

view.setDataRoot(self.modelRoot)

view.getCentralWidget().setDataRoot(self.modelRoot)

return view

class KkitEditorView(MooseEditorView):

"""Default editor.

TODO: Implementation - display moose element tree as a tree or as

boxes inside boxes

"""

def __init__(self, plugin):

MooseEditorView.__init__(self, plugin)

'''

self.insertMenu = QtGui.QMenu('Insert')

sortList = ['CubeMesh','CylMesh','Pool','FuncPool','SumFunc','Reac','Enz','MMenz','StimulusTable','Table']

for slist in sortList:

action = QtGui.QAction(moose.element('/classes/'+slist).name, self.insertMenu)

self._toolBars.append(action)

'''

self.fileinsertMenu = QtGui.QMenu('&File')

if not hasattr(self,'SaveModelAction'):

self.saveModelAction = QtGui.QAction('SaveToSBMLFile', self)

self.saveModelAction.setShortcut(QtGui.QApplication.translate("MainWindow", "Ctrl+S", None, QtGui.QApplication.UnicodeUTF8))

self.connect(self.saveModelAction, QtCore.SIGNAL('triggered()'), self.SaveModelDialogSlot)

self.fileinsertMenu.addAction(self.saveModelAction)

self._menus.append(self.fileinsertMenu)

def SaveModelDialogSlot(self):

type_sbml = 'SBML'

print " here in saveModelDialog"

filters = {'SBML(*.xml)': type_sbml}

filename,filter_ = QtGui.QFileDialog.getSaveFileNameAndFilter(None,'Save File','',';;'.join(filters))

extension = ""

if str(filename).rfind('.') != -1:

filename = filename[:str(filename).rfind('.')]

if str(filter_).rfind('.') != -1:

extension = filter_[str(filter_).rfind('.'):len(filter_)-1]

if filename:

filename = filename+extension

if filters[str(filter_)] == 'SBML':

print "here",filename," ",self.plugin.modelRoot

moose.writeSBML(str(filename),self.plugin.modelRoot)

def getToolPanes(self):

return super(KkitEditorView, self).getToolPanes()

def getLibraryPane(self):

return super(KkitEditorView, self).getLibraryPane()

def getOperationsWidget(self):

return super(KkitEditorView, self).getOperationsPane()

def getToolBars(self):

return self._toolBars

def getCentralWidget(self):

if self._centralWidget is None:

#self._centralWidget = EditorWidgetBase()

self._centralWidget = KineticsWidget()

#print "getCentrelWidget",self.plugin.modelRoot

self._centralWidget.setModelRoot(self.plugin.modelRoot)

return self._centralWidget

class KineticsWidget(EditorWidgetBase):

def __init__(self, *args):

EditorWidgetBase.__init__(self, *args)

self.setAcceptDrops(True)

self.border = 10

self.sceneContainer = QtGui.QGraphicsScene(self)

self.sceneContainer.setSceneRect(self.sceneContainer.itemsBoundingRect())

self.sceneContainer.setBackgroundBrush(QtGui.QColor(230,220,219,120))

self.insertMenu = QtGui.QMenu('&Insert')

self._menus.append(self.insertMenu)

self.insertMapper = QtCore.QSignalMapper(self)

classlist = ['CubeMesh','CylMesh','Pool','FuncPool','SumFunc','Reac','Enz','MMenz','StimulusTable','Table']

insertMapper, actions = self.getInsertActions(classlist)

for action in actions:

self.insertMenu.addAction(action)

def getToolBars(self):

if not hasattr(self, '_insertToolBar'):

self._insertToolBar = QtGui.QToolBar('Insert')

self._toolBars.append(self._insertToolBar)

for action in self.insertMenu.actions():

button = MToolButton()

button.setDefaultAction(action)

self._insertToolBar.addWidget(button)

return self._toolBars

def sizeHint(self):

return QtCore.QSize(800,400)

def updateModelView(self):

#print "update model view",self.modelRoot

if self.modelRoot == '/':

m = wildcardFind('/##[ISA=ChemCompt]')

else:

m = wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]')

#print "111",self.modelRoot,m

if not m:

# when we want an empty GraphicView while creating new model,

# then remove all the view and add an empty view

if hasattr(self, 'view') and isinstance(self.view, QtGui.QWidget):

self.layout().removeWidget(self.view)

self.view = GraphicalView(self.sceneContainer,self.border,self)

self.layout().addWidget(self.view)

else:

# maxmium and minimum coordinates of the objects specified in kkit file.

self.xmin = 0.0

self.xmax = 1.0

self.ymin = 0.0

self.ymax = 1.0

self.autoCordinatepos = {}

self.sceneContainer.clear()

# TODO: size will be dummy at this point, but I need the availiable size from the Gui

self.size = QtCore.QSize(1024 ,768)

#self.size = QtCore.QSize(300,400)

self.autocoordinates = False

# pickled the color map file """

colormap_file = open(os.path.join(config.settings[config.KEY_COLORMAP_DIR], 'rainbow2.pkl'),'rb')

self.colorMap = pickle.load(colormap_file)

colormap_file.close()

# Compartment and its members are setup """

self.meshEntry,self.xmin,self.xmax,self.ymin,self.ymax,self.noPositionInfo = setupMeshObj(self.modelRoot)

# srcdesConnection dictonary will have connection information between src and des """

self.srcdesConnection = {}

setupItem(self.modelRoot,self.srcdesConnection)

if self.noPositionInfo:

self.autocoordinates = True

QtGui.QMessageBox.warning(self,

'No coordinates found for the model',

'\n Automatic layouting will be done')

#raise Exception('Unsupported kkit version')

self.xmin,self.xmax,self.ymin,self.ymax,self.autoCordinatepos = autoCoordinates(self.meshEntry,self.srcdesConnection)

# Scale factor to translate the x -y position to fit the Qt graphicalScene, scene width. """

if self.xmax-self.xmin != 0:

self.xratio = (self.size.width()-10)/(self.xmax-self.xmin)

else: self.xratio = self.size.width()-10

if self.ymax-self.ymin:

self.yratio = (self.size.height()-10)/(self.ymax-self.ymin)

else: self.yratio = (self.size.height()-10)

#A map b/w moose compartment key with QGraphicsObject

self.qGraCompt = {}

#A map between mooseId of all the mooseObject (except compartment) with QGraphicsObject

self.mooseId_GObj = {}

self.border = 5

self.arrowsize = 2

self.iconScale = 1

self.defaultComptsize = 5

self.itemignoreZooming = False

self.lineItem_dict = {}

self.object2line = defaultdict(list)

# Compartment and its members are put on the qgraphicsscene

self.mooseObjOntoscene()

# All the moose Object are connected for visualization

self.drawLine_arrow(itemignoreZooming=False)

if hasattr(self, 'view') and isinstance(self.view, QtGui.QWidget):

self.layout().removeWidget(self.view)

self.view = GraphicalView(self.sceneContainer,self.border,self)

hLayout = QtGui.QGridLayout(self)

self.setLayout(hLayout)

hLayout.addWidget(self.view)

#self.layout().addWidget(self.view)

def mooseObjOntoscene(self):

# All the compartments are put first on to the scene \

# Need to do: Check With upi if empty compartments exist

for cmpt in sorted(self.meshEntry.iterkeys()):

self.createCompt(cmpt)

self.qGraCompt[cmpt]

#comptRef = self.qGraCompt[cmpt]

#Enzymes of all the compartments are placed first, \

# so that when cplx (which is pool object) queries for its parent, it gets its \

# parent enz co-ordinates with respect to QGraphicsscene """

for cmpt,memb in self.meshEntry.items():

for enzObj in find_index(memb,'enzyme'):

enzinfo = enzObj.path+'/info'

if enzObj.className == 'ZEnz':

enzItem = EnzItem(enzObj,self.qGraCompt[cmpt])

else:

enzItem = MMEnzItem(enzObj,self.qGraCompt[cmpt])

self.setupDisplay(enzinfo,enzItem,"enzyme")

self.setupSlot(enzObj,enzItem)

for cmpt,memb in self.meshEntry.items():

for poolObj in find_index(memb,'pool'):

poolinfo = poolObj.path+'/info'

poolItem = PoolItem(poolObj,self.qGraCompt[cmpt])

self.setupDisplay(poolinfo,poolItem,"pool")

self.setupSlot(poolObj,poolItem)

for cplxObj in find_index(memb,'cplx'):

cplxinfo = (cplxObj[0].parent).path+'/info'

cplxItem = CplxItem(cplxObj,self.mooseId_GObj[element(cplxObj[0]).parent.getId()])

self.setupDisplay(cplxinfo,cplxItem,"cplx")

self.setupSlot(cplxObj,cplxItem)

for reaObj in find_index(memb,'reaction'):

reainfo = reaObj.path+'/info'

reaItem = ReacItem(reaObj,self.qGraCompt[cmpt])

self.setupDisplay(reainfo,reaItem,"reaction")

self.setupSlot(reaObj,reaItem)

for tabObj in find_index(memb,'table'):

tabinfo = tabObj.path+'/info'

tabItem = PoolItem(tabObj,self.qGraCompt[cmpt])

self.setupDisplay(tabinfo,tabItem,"tab")

self.setupSlot(tabObj,tabItem)

# compartment's rectangle size is calculated depending on children

for k, v in self.qGraCompt.items():

rectcompt = v.childrenBoundingRect()

v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20))

v.setPen(QtGui.QPen(Qt.QColor(66,66,66,100), 5, Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin))

v.cmptEmitter.connect(v.cmptEmitter,QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),self.positionChange)

v.cmptEmitter.connect(v.cmptEmitter,QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),self.objectEditSlot)

def createCompt(self,key):

self.new_Compt = ComptItem(self,0,0,0,0,key)

self.qGraCompt[key] = self.new_Compt

self.new_Compt.setRect(10,10,10,10)

self.sceneContainer.addItem(self.new_Compt)

def setupDisplay(self,info,graphicalObj,objClass):

xpos,ypos = self.positioninfo(info)

# For Reaction and Complex object I have skipped the process to get the facecolor and background color as \

# we are not using these colors for displaying the object so just passing dummy color white

if( (objClass == "reaction" ) or (objClass == "cplx")):

textcolor,bgcolor = "white","white"

elif objClass == "tab":

textcolor,bgcolor = getColor(info,self.colorMap)

else:

textcolor,bgcolor = getColor(info,self.colorMap)

graphicalObj.setDisplayProperties(xpos,ypos,textcolor,bgcolor)

def positioninfo(self,iteminfo):

if self.noPositionInfo:

try:

# kkit does exist item's/info which up querying for parent.path gives the information of item's parent

x,y = self.autoCordinatepos[(element(iteminfo).parent).path]

except:

# But in Cspace reader doesn't create item's/info, up on querying gives me the error which need to change\

# in ReadCspace.cpp, at present i am taking care b'cos i don't want to pass just the item where I need to check\

# type of the object (rea,pool,enz,cplx,tab) which I have already done.

parent, child = posixpath.split(iteminfo)

x,y = self.autoCordinatepos[parent]

ypos = (y-self.ymin)*self.yratio

else:

x = float(element(iteminfo).getField('x'))

y = float(element(iteminfo).getField('y'))

#Qt origin is at the top-left corner. The x values increase to the right and the y values increase downwards \

#as compared to Genesis codinates where origin is center and y value is upwards, that is why ypos is negated

ypos = -(y-self.ymin)*self.yratio

xpos = (x-self.xmin)*self.xratio

return(xpos,ypos)

def setupSlot(self,mooseObj,qgraphicItem):

self.mooseId_GObj[element(mooseObj).getId()] = qgraphicItem

qgraphicItem.connect(qgraphicItem,QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),self.positionChange)

qgraphicItem.connect(qgraphicItem,QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),self.objectEditSlot)

def updateItemSlot(self, mooseObject):

#This is overridden by derived classes to connect appropriate

#slot for updating the display item.

#In this case if the name is updated from the keyboard both in mooseobj and gui gets updation

changedItem = ''

for item in self.sceneContainer.items():

if isinstance(item,PoolItem):

if mooseObject.getId() == element(item.mobj).getId():

item.updateSlot()

#once the text is edited in editor, laydisplay gets updated in turn resize the length, positionChanged signal shd be emitted

self.positionChange(mooseObject)

def positionChange(self,mooseObject):

#If the item position changes, the corresponding arrow's are calculated

if isinstance(element(mooseObject),CubeMesh):

for k, v in self.qGraCompt.items():

mesh = mooseObject.path+'/mesh[0]'

if k.path == mesh:

for rectChilditem in v.childItems():

self.updateArrow(rectChilditem)

else:

mobj = self.mooseId_GObj[mooseObject.getId()]

self.updateArrow(mobj)

for k, v in self.qGraCompt.items():

rectcompt = v.childrenBoundingRect()

v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20))

def emitItemtoEditor(self,mooseObject):

#self.emit(QtCore.SIGNAL("itemPressed(PyQt_PyObject)"),mooseObject)

self.editObject.emit(mooseObject.path)

def drawLine_arrow(self, itemignoreZooming=False):

for inn,out in self.srcdesConnection.items():

# self.srcdesConnection is dictionary which contains key,value \

# key is Enzyme or Reaction and value [[list of substrate],[list of product]] (tuple)

# key is FuncBase and value is [list of pool] (list)

#src = self.mooseId_GObj[inn]

if isinstance(out,tuple):

if len(out[0])== 0:

print inn.className + ':' +inn[0].name+ " doesn't output message"

else:

src = self.mooseId_GObj[inn]

for items in (items for items in out[0] ):

des = self.mooseId_GObj[element(items[0]).getId()]

self.lineCord(src,des,items,itemignoreZooming)

if len(out[1]) == 0:

print inn.className + ':' +inn[0].name+ " doesn't output message"

else:

for items in (items for items in out[1] ):

des = self.mooseId_GObj[element(items[0]).getId()]

self.lineCord(src,des,items,itemignoreZooming)

elif isinstance(out,list):

if len(out) == 0:

print "Func pool doesn't have sumtotal"

else:

src = self.mooseId_GObj[element(inn).getId()]

for items in (items for items in out ):

des = self.mooseId_GObj[element(items[0]).getId()]

self.lineCord(src,des,items,itemignoreZooming)

def lineCord(self,src,des,type_no,itemignoreZooming):

endtype = type_no[1]

line = 0

if (src == "") and (des == ""):

print "Source or destination is missing or incorrect"

return

srcdes_list = [src,des,endtype,line]

arrow = calcArrow(srcdes_list,itemignoreZooming,self.iconScale)

self.drawLine(srcdes_list,arrow)

while(type_no[2] > 1 and line <= (type_no[2]-1)):

srcdes_list =[src,des,endtype,line]

arrow = calcArrow(srcdes_list,itemignoreZooming,self.iconScale)

self.drawLine(srcdes_list,arrow)

line = line +1

if type_no[2] > 5:

print "Higher order reaction will not be displayed"

def drawLine(self,srcdes_list,arrow):

src = srcdes_list[0]

des = srcdes_list[1]

endtype = srcdes_list[2]

line = srcdes_list[3]

source = element(next((k for k,v in self.mooseId_GObj.items() if v == src), None))

for l,v,o in self.object2line[src]:

if v == des and o ==line:

l.setPolygon(arrow)

arrowPen = l.pen()

arrowPenWidth = self.arrowsize*self.iconScale

arrowPen.setColor(l.pen().color())

arrowPen.setWidth(arrowPenWidth)

l.setPen(arrowPen)

return

qgLineitem = self.sceneContainer.addPolygon(arrow)

pen = QtGui.QPen(QtCore.Qt.green, 0, Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin)

pen.setWidth(self.arrowsize)

#pen.setCosmetic(True)

# Green is default color moose.ReacBase and derivatives - already set above

if isinstance(source, EnzBase):

if ( (endtype == 's') or (endtype == 'p')):

pen.setColor(QtCore.Qt.red)

elif(endtype != 'cplx'):

p1 = (next((k for k,v in self.mooseId_GObj.items() if v == src), None))

pinfo = p1.path+'/info'

color,bgcolor = getColor(pinfo,self.colorMap)

pen.setColor(color)

elif isinstance(source, moose.PoolBase):

pen.setColor(QtCore.Qt.blue)

elif isinstance(source,moose.StimulusTable):

pen.setColor(QtCore.Qt.yellow)

self.lineItem_dict[qgLineitem] = srcdes_list

self.object2line[ src ].append( ( qgLineitem, des,line) )

self.object2line[ des ].append( ( qgLineitem, src,line ) )

qgLineitem.setPen(pen)

def updateArrow(self,qGTextitem):

#if there is no arrow to update then return

if qGTextitem not in self.object2line:

return

listItem = self.object2line[qGTextitem]

for ql, va,order in self.object2line[qGTextitem]:

srcdes = []

srcdes = self.lineItem_dict[ql]

# 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):

self.cplxUpdatearrow(srcdes[0])

elif( type(srcdes[1]) == EnzItem):

self.cplxUpdatearrow(srcdes[1])

# For calcArrow(src,des,endtype,itemignoreZooming) is to be provided

arrow = calcArrow(srcdes,self.itemignoreZooming,self.iconScale)

ql.setPolygon(arrow)

def cplxUpdatearrow(self,srcdes):

# srcdes which is 'EnzItem' from this,get ChildItems are retrived (b'cos cplx is child of zombieEnz)

#And cplxItem is passed for updatearrow

#Note: Here at this point enzItem has just one child which is cplxItem and childItems returns, PyQt4.QtGui.QGraphicsEllipseItem,CplxItem

#Assuming CplxItem is always[1], but still check if not[0], if something changes in structure one need to keep an eye.

if (srcdes.childItems()[1],CplxItem):

self.updateArrow(srcdes.childItems()[1])

else:

self.updateArrow(srcdes.childItems()[0])

def keyPressEvent(self,event):

# key1 = event.key() # key event does not distinguish between capital and non-capital letters

key = event.text().toAscii().toHex()

if key == '41': # 'A' fits the view to iconScale factor

itemignoreZooming = False

self.updateItemTransformationMode(itemignoreZooming)

self.view.fitInView(self.sceneContainer.itemsBoundingRect().x()-10,self.sceneContainer.itemsBoundingRect().y()-10,self.sceneContainer.itemsBoundingRect().width()+20,self.sceneContainer.itemsBoundingRect().height()+20,Qt.Qt.IgnoreAspectRatio)

self.drawLine_arrow(itemignoreZooming=False)

elif (key == '2e'): # '.' key, lower case for '>' zooms in

self.view.scale(1.1,1.1)

elif (key == '2c'): # ',' key, lower case for '<' zooms in

self.view.scale(1/1.1,1/1.1)

elif (key == '3c'): # '<' key. zooms-in to iconScale factor

self.iconScale *= 0.8

self.updateScale( self.iconScale )

elif (key == '3e'): # '>' key. zooms-out to iconScale factor

self.iconScale *= 1.25

self.updateScale( self.iconScale )

elif (key == '61'): # 'a' fits the view to initial value where iconscale=1

self.iconScale = 1

self.updateScale( self.iconScale )

def updateItemTransformationMode(self, on):

for v in self.sceneContainer.items():

if( not isinstance(v,ComptItem)):

#if ( isinstance(v, PoolItem) or isinstance(v, ReacItem) or isinstance(v, EnzItem) or isinstance(v, CplxItem) ):

if isinstance(v,KineticsDisplayItem):

v.setFlag(QtGui.QGraphicsItem.ItemIgnoresTransformations, on)

def updateScale( self, scale ):

for item in self.sceneContainer.items():

if isinstance(item,KineticsDisplayItem):

item.refresh(scale)

#iteminfo = item.mobj.path+'/info'

#xpos,ypos = self.positioninfo(iteminfo)

xpos = item.scenePos().x()

ypos = item.scenePos().y()

if isinstance(item,ReacItem) or isinstance(item,EnzItem) or isinstance(item,MMEnzItem):

item.setGeometry(xpos,ypos,

item.gobj.boundingRect().width(),

item.gobj.boundingRect().height())

elif isinstance(item,CplxItem):

item.setGeometry(item.gobj.boundingRect().width()/2,item.gobj.boundingRect().height(),

item.gobj.boundingRect().width(),

item.gobj.boundingRect().height())

elif isinstance(item,PoolItem):

item.setGeometry(xpos, ypos,item.gobj.boundingRect().width()

+PoolItem.fontMetrics.width(' '),

item.gobj.boundingRect().height())

item.bg.setRect(0, 0, item.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' '), item.gobj.boundingRect().height())

self.drawLine_arrow(itemignoreZooming=False)

for k, v in self.qGraCompt.items():

rectcompt = v.childrenBoundingRect()

comptPen = v.pen()

comptWidth = self.defaultComptsize*self.iconScale

comptPen.setWidth(comptWidth)

v.setPen(comptPen)

v.setRect(rectcompt.x()-comptWidth,rectcompt.y()-comptWidth,(rectcompt.width()+2*comptWidth),(rectcompt.height()+2*comptWidth))

if __name__ == "__main__":

app = QtGui.QApplication(sys.argv)

size = QtCore.QSize(1024 ,768)

modelPath = 'Kholodenko'

#modelPath = 'acc61'

#modelPath = 'acc8'

modelPath = '3ARECB'

#modelPath = '3AreacB'

modelPath = '5AreacB'

itemignoreZooming = False

try:

filepath = '../../Demos/Genesis_files/'+modelPath+'.g'

#filepath = '/home/harsha/genesis_files/gfile/'+modelPath+'.g'

print filepath

f = open(filepath, "r")

loadModel(filepath,'/'+modelPath)

moose.le('/'+modelPath+'/kinetics')

dt = KineticsWidget()

dt.modelRoot ='/'+modelPath

''' Loading moose signalling model in python '''

#execfile('/home/harsha/BuildQ/Demos/Genesis_files/scriptKineticModel.py')

#dt.modelRoot = '/model'

dt.updateModelView()

dt.show()

except IOError, what:

(errno, strerror) = what

print "Error number",errno,"(%s)" %strerror

sys.exit(0)

sys.exit(app.exec_())

moose-gui/plugins/buildkkit.py at master · BhallaLab/moose-gui · GitHub

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