diff --git a/.travis.yml b/.travis.yml
index 15779bf198d587255777bc0c0afe4c636ee06f89..b296745728e24698a436b5a6a30529f0504037cd 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -13,7 +13,7 @@ install:
- sudo apt-get -y update
- sudo apt-get -y --force-yes install python3 python-pip
- sudo apt-get -y --force-yes install moose
- - sudo pip install python-libsbml
+ - sudo -H pip install python-libsbml
script:
- # Making sure no python incompatible file is added.
diff --git a/PlotWidgetContainer.py b/PlotWidgetContainer.py
index f42e0a87e27ba9fe891b53344957d2f43a29b402..d51ab81e106837737f6d422d6282ed01af263395 100644
--- a/PlotWidgetContainer.py
+++ b/PlotWidgetContainer.py
@@ -4,14 +4,14 @@ from __future__ import print_function
"""
"""
-
-__author__ = "Aviral Goel"
__credits__ = ["Upi Lab"]
+__author__ = "Aviral Goel"
__license__ = "GPL3"
__version__ = "1.0.0"
-__maintainer__ = "Aviral Goel"
+__maintainer__ = "Aviral Goel", "HarshaRani"
__email__ = "goel.aviral@gmail.com"
__status__ = "Development"
+__updated__ = "Jul 26 2017"
import sys
@@ -49,6 +49,7 @@ class PlotWidgetContainer(QWidget):
self.model = moose.element(self.modelRoot)
if self.modelRoot != "/":
+ self.modelRoot = self.findModelPath(self.modelRoot)
if moose.exists(modelRoot + "/data"):
self.data = moose.element(self.modelRoot + "/data")
else:
@@ -87,6 +88,17 @@ class PlotWidgetContainer(QWidget):
if len(self.data.children) == 0:
self.addPlotWidget()
+ def mooseIsInstance(self,element, classNames):
+ return moose.element(element).__class__.__name__ in classNames
+
+
+ def findModelPath(self,element):
+ child = element
+ while not self.mooseIsInstance(element, "Shell"):
+ child = moose.element(element).path
+ element = moose.element(element).parent
+ return child
+
def deleteWidget(self, graphWidget):
# print("Deleted => ", graphWidget)
self.graphWidgets.remove(graphWidget)
diff --git a/defaults.py b/defaults.py
index 458f7b389e3f566a83ce0e2fc6c98cfaa3e1ac74..f7a513804c8fa5024216e12b00d46b5e7c4e8ceb 100644
--- a/defaults.py
+++ b/defaults.py
@@ -1,3 +1,11 @@
+__credits__ = ["Upi Lab"]
+__author__ = "Subhasis"
+__license__ = "GPL3"
+__version__ = "1.0.0"
+__maintainer__ = "Subhasis", "HarshaRani","Aviral Goel"
+__email__ = "goel.aviral@gmail.com"
+__status__ = "Development"
+__updated__ = "Jul 26 2017"
PLOT_FIELDS={
'LeakyIaF':['Vm'],
@@ -11,8 +19,11 @@ PLOT_FIELDS={
FIELD_UNITS={
'volume':'m3',
'Kd' : 'mM',
- 'Km':'mM',
+ 'Km' :'mM',
'kcat':'s-1',
+ 'k1' :'1/# s',
+ 'k2' :'s-1',
+ 'k3' :'s-1',
'Vm':'V',
'conc':'mM',
'concInit':'mM',
diff --git a/mgui.py b/mgui.py
index 9f201303e2db36f325e27661637b37fbcfb7504a..24d2bf83bc575b109adbda5837de124d4a8cc587 100644
--- a/mgui.py
+++ b/mgui.py
@@ -2,13 +2,13 @@
#
# Filename: mgui.py
# Description:
-# Author:
-# Maintainer:
+# Author: "Subhasis", "HarshaRani","Aviral Goel"
+# Maintainer: HarshaRani
# Created: Mon Nov 12 09:38:09 2012 (+0530)
# Version:
-# Last-Updated: Fri Oct 30 11:54:33 2015 (+0530)
+# Last-Updated: Thu Oct 5 14:54:33 2017 (+0530)
# By: Harsha
-# Update #: 1338
+# Update #:
# URL:
# Keywords:
# Compatibility:
@@ -43,6 +43,10 @@
#
#
+''''
+Oct 5: clean up with round trip of dialog_exe
+
+'''
# Code:
import imp
import inspect
@@ -206,7 +210,7 @@ class MWindow(QtGui.QMainWindow):
("Fig5A (20s)", "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5A.py"),
("Fig5BCD (240s)" , "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5BCD.py"),
("Fig6A (60s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/Fig6A.py" ),
- ("Reduced6 (200s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py"),
+ ("ReducedModel (200s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py"),
("Squid" , "../moose-examples/squid/squid_demo.py")
])
layout.setContentsMargins(QtCore.QMargins(20,20,20,20))
@@ -246,7 +250,7 @@ class MWindow(QtGui.QMainWindow):
button.setToolTip("<span style=\"color:black;\">Illustrates building a panel of multiscale models to test neuronal plasticity in different contexts</span>")
elif k[0] == "Fig6A (60s)":
button.setToolTip("<span style=\"color:black;\">This LIF network with Ca plasticity is based on: Memory Maintenance in Synapses with Calcium-Based Plasticity in the Presence of Background Activity PLOS Computational Biology, 2014</span>")
- elif k[0] == "Reduced6 (200s)":
+ elif k[0] == "ReducedModel (200s)":
button.setToolTip("<span style=\"color:black;\">This is the Reduced version of LIF network with Ca plasticity model based on: Memory Maintenance in Synapses with Calcium-Based Plasticity in the Presence of Background Activity PLOS Computational Biology, 2014</span>")
elif k[0] == "Squid":
button.setToolTip("<span style=\"color:black;\">squid Demo</span>")
@@ -258,7 +262,7 @@ class MWindow(QtGui.QMainWindow):
layout4.addWidget(button)
elif k[0] in ["Fig5A (20s)","Fig5BCD (240s)"]:
layout5.addWidget(button)
- elif k[0] in ["Fig6A (60s)","Reduced6 (200s)"]:
+ elif k[0] in ["Fig6A (60s)","ReducedModel (200s)"]:
layout6.addWidget(button)
elif k[0] in ["Squid"]:
layout7.addWidget(button)
@@ -292,6 +296,7 @@ class MWindow(QtGui.QMainWindow):
self.popup.hide()
abspath = os.path.abspath(filepath)
directory, modulename = os.path.split(abspath)
+
modelName = os.path.splitext(modulename)[0]
ret = loadFile(str(abspath),'%s' %(modelName),solver,merge=False)
self.setPlugin("kkit", ret["model"].path)
@@ -641,22 +646,64 @@ class MWindow(QtGui.QMainWindow):
("Fig5A (20s)", "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5A.py"),
("Fig5BCD (240s)" , "../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5BCD.py"),
("Fig6A (60s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/Fig6A.py" ),
- ("Reduced6 (200s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py"),
+ ("ReducedModel (200s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py"),
("Squid" , "../moose-examples/squid/squid_demo.py")
])
- self.subMenu = QtGui.QMenu('Paper_2015_Demos')
+ self.subMenu = QtGui.QMenu('Demos')
for i in range(0,len(self.menuitems)):
k = self.menuitems.popitem(0)
- t = "self."+k[0]+"Action"
- t = QtGui.QAction(k[0],self)
- self.subMenu.addAction(t)
- if k[0] == "Fig3C_Gsl (2s)":
- t.connect(t,QtCore.SIGNAL('triggered()'),lambda script = k[1]: self.run_genesis_script(script,"gsl"))
+ if k[0] == "Fig2C (6s)":
+ self.Fig2Caction = QtGui.QAction('Fig2C (6s)', self)
+ self.Fig2Caction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig2_elecModels/Fig2C.py'))
+ self.subMenu.addAction(self.Fig2Caction)
+ elif k[0] == "Fig2D (35s)":
+ self.Fig2Daction = QtGui.QAction('Fig2D (35s)', self)
+ self.Fig2Daction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig2_elecModels/Fig2D.py'))
+ self.subMenu.addAction(self.Fig2Daction)
+ elif k[0] == "Fig2E (5s)":
+ self.Fig2Eaction = QtGui.QAction('Fig2E (5s)', self)
+ self.Fig2Eaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig2_elecModels/Fig2E.py'))
+ self.subMenu.addAction(self.Fig2Eaction)
elif k[0] == "Fig3B_Gssa (2s)":
- t.connect(t,QtCore.SIGNAL('triggered()'),lambda script = k[1]: self.run_genesis_script(script,"gssa"))
+ self.Fig3B_Gssaaction = QtGui.QAction('Fig3B_Gssa (2s)', self)
+ self.Fig3B_Gssaaction.triggered.connect(lambda :self.run_genesis_script('../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g',"gssa"))
+ self.subMenu.addAction(self.Fig3B_Gssaaction)
+ elif k[0] == "Fig3C_Gsl (2s)":
+ self.Fig3C_Gslaction = QtGui.QAction('Fig3C_Gsl (2s)', self)
+ self.Fig3C_Gslaction.triggered.connect(lambda :self.run_genesis_script('../moose-examples/paper-2015/Fig3_chemModels/Fig3ABC.g',"gsl"))
+ self.subMenu.addAction(self.Fig3C_Gslaction)
+ elif k[0] == "Fig3D (1s)":
+ self.Fig3Daction = QtGui.QAction('Fig3D (1s)', self)
+ self.Fig3Daction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig3_chemModels/Fig3D.py'))
+ self.subMenu.addAction(self.Fig3Daction)
+ elif k[0] == "Fig4B (10s)":
+ self.Fig4Baction = QtGui.QAction('Fig4B (10s)', self)
+ self.Fig4Baction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig4_ReacDiff/Fig4B.py'))
+ self.subMenu.addAction(self.Fig4Baction)
+ elif k[0] == "Fig4K":
+ self.Fig4Kaction = QtGui.QAction('Fig4K', self)
+ self.Fig4Kaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig4_ReacDiff/rxdSpineSize.py'))
+ self.subMenu.addAction(self.Fig4Kaction)
+ elif k[0] == "Fig5A (20s)":
+ self.Fig5Aaction = QtGui.QAction('Fig5A (20s)', self)
+ self.Fig5Aaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5A.py'))
+ self.subMenu.addAction(self.Fig5Aaction)
+ elif k[0] == "Fig5BCD (240s)":
+ self.Fig5BCDaction = QtGui.QAction('Fig5BCD (240s)', self)
+ self.Fig5BCDaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig5_CellMultiscale/Fig5BCD.py'))
+ self.subMenu.addAction(self.Fig5BCDaction)
+ elif k[0] == "Fig6A (60s)":
+ self.Fig6Aaction = QtGui.QAction('Fig6A (60s)', self)
+ self.Fig6Aaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig6_NetMultiscale/Fig6A.py'))
+ self.subMenu.addAction(self.Fig6Aaction)
+ elif k[0] == "ReducedModel (200s)":
+ self.ReducedModelaction = QtGui.QAction('ReducedModel (200s)', self)
+ self.ReducedModelaction.triggered.connect(lambda :self.run_python_script('../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py'))
+ self.subMenu.addAction(self.ReducedModelaction)
else:
- t.connect(t,QtCore.SIGNAL('triggered()'),lambda : self.run_python_script(k[1]))
- self.subMenu.addAction(t)
+ self.Squidaction = QtGui.QAction('Squid', self)
+ self.Squidaction.triggered.connect(lambda :self.run_python_script('../moose-examples/squid/squid_demo.py'))
+ self.subMenu.addAction(self.Squidaction)
self.fileMenu.addMenu(self.subMenu)
if not hasattr(self,'loadedModels'):
@@ -1030,6 +1077,11 @@ class MWindow(QtGui.QMainWindow):
self.objectEditDockWidget.setObject(mobj)
self.objectEditDockWidget.setVisible(visible)
+ # def objectEditClearSlot(self):
+ # #clearning the views which is stored
+ # self.objectEditDockWidget.clearDict()
+
+
def loadedModelsAction(self,modelPath,pluginName):
#Harsha: added under file Menu, Recently Loaded Models
#All the previously loaded chemical models, solver's and table's ticks are made -1
@@ -1105,20 +1157,31 @@ class MWindow(QtGui.QMainWindow):
ret = []
ret,pluginName = self.checkPlugin(dialog)
if pluginName == 'kkit':
- compt = moose.wildcardFind(ret['model'].path+'/##[ISA=ChemCompt]')
- if not len(compt):
- reply = QtGui.QMessageBox.question(self, "Model is empty","Model has no compartment, atleast one compartment should exist to display the widget\n Do you want another file",
- QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
- if reply == QtGui.QMessageBox.Yes:
- dialog = LoaderDialog(self,self.tr('Load model from file'))
- if dialog.exec_():
- ret,pluginName = self.checkPlugin(dialog)
- ret,valid = self.dialog_check(ret)
- else:
- QtGui.QApplication.restoreOverrideCursor()
+ if (ret['subtype'] == 'sbml' and ret['foundlib'] == False):
+ reply = QtGui.QMessageBox.question(self, "python-libsbml is not found.","\n Read SBML is not possible.\n This can be installed using \n \n pip python-libsbml or \n apt-get install python-libsbml",
+ QtGui.QMessageBox.Ok)
+ if reply == QtGui.QMessageBox.Ok:
+ QtGui.QApplication.restoreOverrideCursor()
return
else:
- valid = True
+ if ret['loaderror'] != "":
+ reply = QtGui.QMessageBox.question(self, "Model can't be loaded", ret['loaderror']+" \n \n Do you want another file",
+ QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
+ if reply == QtGui.QMessageBox.Yes:
+ dialog = LoaderDialog(self,self.tr('Load model from file'))
+ if dialog.exec_():
+ valid = False
+ ret = []
+ pluginName = None
+ ret,pluginName = self.checkPlugin(dialog)
+
+ valid, ret = self.dialog_check(ret)
+ else:
+ QtGui.QApplication.restoreOverrideCursor()
+ return valid
+ else:
+
+ valid = True
if valid == True:
modelAnno = moose.Annotator(ret['model'].path+'/info')
if ret['subtype']:
@@ -1160,34 +1223,47 @@ class MWindow(QtGui.QMainWindow):
self.objectEditSlot('/',False)
#if subtype is None, in case of cspace then pluginLookup = /cspace/None
# which will not call kkit plugin so cleaning to /cspace
- pluginLookup = '%s/%s' % (ret['modeltype'], ret['subtype'])
+ #pluginLookup = '%s/%s' % (ret['modeltype'], ret['subtype'])
try:
pluginName = subtype_plugin_map['%s/%s' % (ret['modeltype'], ret['subtype'])]
except KeyError:
pluginName = 'default'
- print 'Loaded model', ret['model'].path
+ if ret['foundlib']:
+ print ('Loaded model %s' %(ret['model']))
return ret,pluginName
def dialog_check(self,ret):
+ valid = False
pluginLookup = '%s/%s' % (ret['modeltype'], ret['subtype'])
try:
pluginName = subtype_plugin_map['%s/%s' % (ret['modeltype'], ret['subtype'])]
except KeyError:
pluginName = 'default'
+
if pluginName == 'kkit':
- compt = moose.wildcardFind(ret['model'].path+'/##[ISA=ChemCompt]')
- if not len(compt):
- reply = QtGui.QMessageBox.question(self, "Model is empty","Model has no compartment, atleast one compartment should exist to display the widget\n Do you want another file",
- QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
- if reply == QtGui.QMessageBox.Yes:
- dialog = LoaderDialog(self,self.tr('Load model from file'))
- if dialog.exec_():
- ret,pluginName = self.checkPlugin(dialog)
- else:
- QtGui.QApplication.restoreOverrideCursor()
- return
+ if (ret['subtype'] == 'sbml' and ret['foundlib'] == False):
+ reply = QtGui.QMessageBox.question(self, "python-libsbml is not found.","\n Read SBML is not possible.\n This can be installed using \n \n pip python-libsbml or \n apt-get install python-libsbml",
+ QtGui.QMessageBox.Ok)
+ if reply == QtGui.QMessageBox.Ok:
+ QtGui.QApplication.restoreOverrideCursor()
+ return valid, ret
else:
- return ret,True
+ if ret['loaderror'] != "":
+ reply = QtGui.QMessageBox.question(self, "Model can't be loaded", ret['loaderror']+" \n \n Do you want another file",
+ QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
+ if reply == QtGui.QMessageBox.Yes:
+ dialog = LoaderDialog(self,self.tr('Load model from file'))
+ if dialog.exec_():
+ pluginName = None
+ ret,pluginName = self.checkPlugin(dialog)
+ valid,ret = self.dialog_check(ret)
+ else:
+ QtGui.QApplication.restoreOverrideCursor()
+ return valid,ret
+ else:
+ valid = True
+ return valid,ret
+
def newModelDialogSlot(self):
#Harsha: Create a new dialog widget for model building
self.popup.close()
diff --git a/mload.py b/mload.py
index 257daa9410909a3fb8eb877afdf8ef7ff7d125b5..9fc753e64551b388f7b605d0fe326fc75738e930 100644
--- a/mload.py
+++ b/mload.py
@@ -2,12 +2,12 @@
#
# Filename: mload.py
# Description:
-# Author:
-# Maintainer:
+# Author: Subhasis
+# Maintainer:HarshaRani
# Created: Fri Feb 8 09:38:40 2013 (+0530)
# Version:
-# Last-Updated: Wed May 22 12:16:35 2013 (+0530)
-# By: subha
+# Last-Updated: Wed Oct 5 15:16:35 2017 (+0530)
+# By: HarshaRani
# Update #: 213
# URL:
# Keywords:
@@ -44,7 +44,12 @@
#
# Code:
-
+'''
+Oct 5 : check is made for kkit model
+ -- Atleast one compartment should exists
+ -- Atleast 2 pool should exists
+Oct 4 : clean up for python3
+'''
import moose
from moose import neuroml
import mtypes
@@ -118,7 +123,10 @@ def loadFile(filename, target, solver="gsl", merge=True):
modelroot: root element of the model, None if could not be located - as is the case with Python scripts
"""
+ loaderror = ""
num = 1
+ libsfound = True
+ model = '/'
newTarget = target
while moose.exists(newTarget):
newTarget = target + "-" + str(num)
@@ -128,7 +136,7 @@ def loadFile(filename, target, solver="gsl", merge=True):
with open(filename, 'rb') as infile:
istext = mtypes.istextfile(infile)
if not istext:
- print 'Cannot handle any binary formats yet'
+ print ('Cannot handle any binary formats yet')
return None
# parent, child = posixpath.split(target)
# p = moose.Neutral(parent)
@@ -149,31 +157,42 @@ def loadFile(filename, target, solver="gsl", merge=True):
model,modelpath = loadGenCsp(target,filename,solver)
xcord,ycord = [],[]
if moose.exists(moose.element(modelpath).path):
- 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]')
- for p in mObj:
- if not isinstance(moose.element(p.parent),moose.CplxEnzBase):
- xcord.append(moose.element(p.path+'/info').x)
- ycord.append(moose.element(p.path+'/info').y)
- recalculatecoordinatesforKkit(mObj,xcord,ycord)
-
- for ememb in moose.wildcardFind(moose.element(modelpath).path+'/##[ISA=EnzBase]'):
- objInfo = ememb.path+'/info'
- #Enzyme's textcolor (from kkit) will be bgcolor (in moose)
- if moose.exists(objInfo):
- bgcolor = moose.element(objInfo).color
- moose.element(objInfo).color = moose.element(objInfo).textColor
- moose.element(objInfo).textColor = bgcolor
-
- moose.Annotator(moose.element(modelpath).path+'/info').modeltype = "kkit"
- else:
- print " path doesn't exists"
- moose.le(modelpath)
+ process = True
+ compt = len(moose.wildcardFind(modelpath+'/##[ISA=CubeMesh]'))
+ if not compt:
+ loaderror = "Model has no compartment, atleast one compartment should exist to display the widget"
+ process = False
+ else:
+ p = len(moose.wildcardFind(modelpath+'/##[ISA=PoolBase]'))
+ if p < 2:
+ loaderror = "Model has no pool, atleast two pool should exist to display the widget"
+ process = False
+ if process:
+ if moose.exists(moose.element(modelpath).path):
+ 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]')
+ for p in mObj:
+ if not isinstance(moose.element(p.parent),moose.CplxEnzBase):
+ xcord.append(moose.element(p.path+'/info').x)
+ ycord.append(moose.element(p.path+'/info').y)
+ recalculatecoordinatesforKkit(mObj,xcord,ycord)
+
+ for ememb in moose.wildcardFind(moose.element(modelpath).path+'/##[ISA=EnzBase]'):
+ objInfo = ememb.path+'/info'
+ #Enzyme's textcolor (from kkit) will be bgcolor (in moose)
+ if moose.exists(objInfo):
+ bgcolor = moose.element(objInfo).color
+ moose.element(objInfo).color = moose.element(objInfo).textColor
+ moose.element(objInfo).textColor = bgcolor
+ moose.Annotator(moose.element(modelpath).path+'/info').modeltype = "kkit"
+ else:
+ print (" path doesn't exists")
+ moose.le(modelpath)
else:
- print 'Only kkit and prototype files can be loaded.'
-
+ print ('Only kkit and prototype files can be loaded.')
+
elif modeltype == 'cspace':
model,modelpath = loadGenCsp(target,filename)
@@ -205,7 +224,7 @@ def loadFile(filename, target, solver="gsl", merge=True):
# moose.move("cells/", cell.path)
elif subtype == 'sbml':
- foundLibtaSBML_ = False
+ foundLibSBML_ = False
try:
import libsbml
foundLibSBML_ = True
@@ -215,7 +234,7 @@ def loadFile(filename, target, solver="gsl", merge=True):
if target != '/':
if moose.exists(target):
moose.delete(target)
- model = mooseReadSBML(filename,target)
+ model,loaderror = mooseReadSBML(filename,target)
if moose.exists(moose.element(model).path):
moose.Annotator(moose.element(model).path+'/info').modeltype = "sbml"
addSolver(target,'gsl')
@@ -229,7 +248,9 @@ def loadFile(filename, target, solver="gsl", merge=True):
# app.restoreOverrideCursor()
return {'modeltype': modeltype,
'subtype': subtype,
- 'model': model}
+ 'model': model,
+ 'foundlib' : libsfound,
+ 'loaderror' : loaderror}
#
diff --git a/objectedit.py b/objectedit.py
index a98294cc3f3fa619651e8ccf70f011bba1122810..dcb019a4d50d3faaf86e33d5cfdb1265f27302b4 100644
--- a/objectedit.py
+++ b/objectedit.py
@@ -6,7 +6,7 @@
# Maintainer:
# Created: Wed Jun 30 11:18:34 2010 (+0530)
# Version:
-# Last-Updated: Friday May 17 23:45:59 2017 (+0530)
+# Last-Updated: Thu Jul 27 11:05:59 2017 (+0530)
# By: Harsha
# Update #:
# URL:
@@ -193,7 +193,6 @@ class ObjectEditModel(QtCore.QAbstractTableModel):
def setData(self, index, value, role=QtCore.Qt.EditRole):
if not index.isValid() or index.row () >= len(self.fields) or index.column() != 1:
return False
- print(value)
field = self.fields[index.row()]
if (role == QtCore.Qt.CheckStateRole):
if (index.column() == 1):
@@ -236,8 +235,17 @@ class ObjectEditModel(QtCore.QAbstractTableModel):
else:
oldValue = self.mooseObject.getField(field)
- value = type(oldValue)(value)
- tt = self.mooseObject.setField(field, value)
+ if field != "isBuffered":
+ value = type(oldValue)(value)
+ self.mooseObject.setField(field, value)
+ else:
+ if self.mooseObject.className == "ZombiePool" or self.mooseObject.className =="ZombieBufPool":
+ QtGui.QMessageBox.warning(None,'Solver is set, Could not set the value','\n Unset the solver by clicking \n run widget -> Preferences -> Exponential Euler->Apply')
+ else:
+ if value.lower() in ("yes", "true", "t", "1"):
+ self.mooseObject.setField(field, True)
+ else:
+ self.mooseObject.setField(field, False)
self.undoStack.append((index, oldValue))
if field == 'name':
self.emit(QtCore.SIGNAL('objectNameChanged(PyQt_PyObject)'), self.mooseObject)
@@ -247,7 +255,7 @@ class ObjectEditModel(QtCore.QAbstractTableModel):
return True
def undo(self):
- print 'Undo'
+ print ('Undo')
if len(self.undoStack) == 0:
raise Info('No more undo information')
index, oldvalue, = self.undoStack.pop()
@@ -417,7 +425,7 @@ class ObjectEditView(QtGui.QTableView):
self.setColor(getColor(self.model().mooseObject.path+'/info')[1])
except:
pass
- print 'Created view with', mobject
+ print ('Created view with %s' %(mobject))
def setColor(self, color):
self.colorButton.setStyleSheet(
@@ -431,8 +439,6 @@ class ObjectEditView(QtGui.QTableView):
QtGui.QTableView.dataChanged(self, tl, br)
self.viewport().update()
-
-
class ObjectEditDockWidget(QtGui.QDockWidget):
"""A dock widget whose title is set by the current moose
object. Allows switching the moose object. It stores the created
@@ -461,7 +467,8 @@ class ObjectEditDockWidget(QtGui.QDockWidget):
self.setWindowTitle('Edit: %s' % (mobj.path))
# self.view.colorDialog.colorSelected.connect(self.colorChangedEmit)
-
+ # def clearDict(self):
+ # self.view_dict.clear()
def setObject(self, mobj):
element = moose.element(mobj)
diff --git a/plugins/constants.py b/plugins/constants.py
index 558b5fc518e205f7536551e6f3d2580c4b889915..3596f2c5180bb71b02e5d145e3e8470630d6d9e3 100644
--- a/plugins/constants.py
+++ b/plugins/constants.py
@@ -1,16 +1,24 @@
-INVALID = 6
-INTERIOR = 7
-BOUNDARY = 8
-SAME_OBJECT = 9
-OTHER_OBJECT = 10
-NO_OBJECT = 11
-RUBBERBAND_SELECTION = 12
-VALID = 13
+INVALID = 6
+
+INTERIOR = 7
+BOUNDARY = 8
+
+SAME_OBJECT = 9
+OTHER_OBJECT = 10
+NO_OBJECT = 11
+
+RUBBERBAND_SELECTION = 12
+VALID = 13
ITEM = 0
CONNECTOR = 1
CONNECTION = 2
EMPTY = 3
+
COMPARTMENT = 14
COMPARTMENT_BOUNDARY = 4
COMPARTMENT_INTERIOR = 5
+
+GROUP = 15
+GROUP_BOUNDARY = 16
+GROUP_INTERIOR = 17
diff --git a/plugins/default.py b/plugins/default.py
index ccf8846d94ebcdd5197672590f7110283a0d9930..788e8349a82ca1f7d89b155a3a30eef333072a6e 100644
--- a/plugins/default.py
+++ b/plugins/default.py
@@ -6,9 +6,9 @@
# Maintainer:
# Created: Tue Nov 13 15:58:31 2012 (+0530)
# Version:
-# Last-Updated: Thu Jul 18 10:35:00 2013 (+0530)
-# By: subha
-# Update #: 2244
+# Last-Updated: Thu Oct 5 12:35:00 2013 (+0530)
+# By: Harsha
+# Update #:
# URL:
# Keywords:
# Compatibility:
@@ -44,7 +44,11 @@
#
# Code:
+'''
+Oct 5: could not recreate if object already exist in moose which was allowed earlier
+ now if object exist need to use element which is cleaned here
+'''
import sys
import config
import pickle
@@ -331,9 +335,15 @@ class RunView(RunBase):
self.dataRoot = modelRoot + '/data'
else:
self.dataRoot = "/data"
- self.setModelRoot(moose.Neutral(self.plugin.modelRoot).path)
- self.setDataRoot(moose.Neutral('/data').path)
- self.setDataRoot(moose.Neutral(self.plugin.modelRoot).path)
+ if not moose.exists(self.plugin.modelRoot):
+ moose.Neutral(self.plugin.modelroot)
+ self.setModelRoot(moose.element(self.plugin.modelRoot).path)
+ if not moose.exists('/data'):
+ moose.Neutral('/data')
+ self.setDataRoot(moose.element('/data').path)
+ if not moose.exists(self.plugin.modelRoot):
+ moose.Neutral(self.plugin.modelRoot)
+ self.setDataRoot(moose.element(self.plugin.modelRoot).path)
self.plugin.modelRootChanged.connect(self.setModelRoot)
self.plugin.dataRootChanged.connect(self.setDataRoot)
# self.getCentralWidget()
@@ -709,19 +719,34 @@ class SchedulingWidget(QtGui.QWidget):
else:
stoich = moose.Stoich(compt[0].path+'/stoich')
status = int(stoich.status)
+ # Flag to track status of Stoich object.
+ # -1: No path yet assigned.
+ # 0: Success
+ # 1: Warning: Missing reactant in Reac or Enz
+ # 2: Warning: Missing substrate in MMenz
+ # 4: Warning: Compartment not defined
+ # 8: Warning: Neither Ksolve nor Dsolve defined
+ # 16: Warning: No objects found on path
+
# print("Status =>", status)
+
+ if status == 1 or status == 2:
+ nameRE = "\n\nclassName --> parent --> name "
+ for res in moose.wildcardFind(self.modelRoot+'/##[ISA=ReacBase],'+self.modelRoot+'/##[ISA=EnzBase]'):
+ if not len(res.neighbors["sub"]) or not len(res.neighbors["prd"]):
+ nameRE = nameRE+"\n "+res.className + " --> "+res.parent.name+ " --> "+res.name
+
if status == -1:
QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Reaction path not yet assigned.\n ")
return -1
if status == 1:
- QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a reactant in a Reac or Enz.\n ")
+ #QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a reactant in a Reac or Enz.\n ")
+ QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a reactant in %s " %(nameRE))
return 1
elif status == 2:
- QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a substrate in an MMenz.\n ")
+ QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a substrate in an MMenz %s " %(nameRE))
+ #QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing a substrate in an MMenz.\n ")
return 2
- elif status == 3:
- QtGui.QMessageBox.warning(None,"Could not Run the model","Warning: Missing substrates as well as reactants.\n ")
- return 3
elif status == 4:
QtGui.QMessageBox.warning(None,"Could not Run the model"," Warning: Compartment not defined.\n ")
return 4
diff --git a/plugins/kkit.py b/plugins/kkit.py
index 68bfd85ee77dcfb1a38c00ffea00e794363bc74a..b6f7fb5a4a249931a336f7a2e576ab4d6b87bea0 100644
--- a/plugins/kkit.py
+++ b/plugins/kkit.py
@@ -6,19 +6,20 @@ __version__ = "1.0.0"
__maintainer__ = "HarshaRani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
-__updated__ = "Mar 7 2017"
+__updated__ = "Oct 18 2017"
+'''
+
+'''
import math
import sys
from PyQt4 import QtGui, QtCore, Qt
from default import *
from moose import *
-#from moose.genesis import write
from moose import SBML
from moose.genesis.writeKkit import mooseWriteKkit
-#sys.path.append('plugins')
from mplugin import *
from kkitUtil import *
-from kkitQGraphics import PoolItem, ReacItem,EnzItem,CplxItem,ComptItem
+from kkitQGraphics import *
from kkitViewcontrol import *
from kkitCalcArrow import *
from kkitOrdinateUtil import *
@@ -77,11 +78,16 @@ class KkitPlugin(MoosePlugin):
if filters[str(filter_)] == 'SBML':
self.sceneObj = KkitEditorView(self).getCentralWidget().mooseId_GObj
self.coOrdinates = {}
+ self.plugin = KkitEditorView(self).getCentralWidget().plugin
+ self.defaultScenewidth = KkitEditorView(self).getCentralWidget().defaultScenewidth
+ self.defaultSceneheight = KkitEditorView(self).getCentralWidget().defaultSceneheight
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 moose.element(self.plugin.modelRoot+'/info').modeltype == 'kkit':
+ self.coOrdinates[k] = {'x':annoInfo.x*self.defaultScenewidth, 'y':annoInfo.y*self.defaultSceneheight}
+ else:
+ self.coOrdinates[k] = {'x':annoInfo.x, 'y':annoInfo.y}
#writeerror = moose.writeSBML(self.modelRoot,str(filename),self.coOrdinates)
writeerror = -2
conisitencyMessages = ""
@@ -105,12 +111,12 @@ class KkitPlugin(MoosePlugin):
if moose.exists(moose.element(k).path+'/info'):
annoInfo = Annotator(k.path+'/info')
#co-ordinates will be in decimals converting to int which should be b/w 0 to 10
- x = annoInfo.x *10
- y = -annoInfo.y *10
+ x = annoInfo.x * 10
+ y = -annoInfo.y * 10
self.coOrdinates[k] = {'x':x, 'y':y}
- error,writen = mooseWriteKkit(self.modelRoot,str(filename),self.coOrdinates)
- if writen == False:
+ error,written = mooseWriteKkit(self.modelRoot,str(filename),self.coOrdinates)
+ if written == False:
QtGui.QMessageBox.information(None,'Could not save the Model','\nCheck the file')
else:
if error == "":
@@ -329,22 +335,16 @@ class KineticsWidget(EditorWidgetBase):
self.arrowsize = 2
self.reset()
- self.defaultSceneheight = 500
- self.defaultScenewidth = 1000
+ self.defaultSceneheight = 800#1000
+ self.defaultScenewidth = 1000#2400
self.positionInfoExist = True
self.defaultComptsize = 5
self.srcdesConnection = {}
-
+ self.meshEntry = {}
self.mooseId_GObj = {}
self.qGraCompt = {}
self.xyCord = {}
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 = {}
@@ -419,22 +419,50 @@ class KineticsWidget(EditorWidgetBase):
self.m = wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]')
if self.m:
self.srcdesConnection = {}
+ if self.meshEntry:
+ self.meshEntry.clear()
+ else:
+ self.meshEntry = {}
#self.meshEntry.clear= {}
# Compartment and its members are setup
#self.meshEntry,self.xmin,self.xmax,self.ymin,self.ymax,self.noPositionInfo = setupMeshObj(self.modelRoot)
- self.meshEntry,xcord,ycord = setupMeshObj(self.modelRoot)
- self.positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 \
- and len(np.nonzero(ycord)[0]) == 0)
-
+ #self.meshEntry,xcord,ycord = setupMeshObj(self.modelRoot)
+ #self.positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 \
+ # and len(np.nonzero(ycord)[0]) == 0)
+ self.objPar,self.meshEntry,self.xmin,self.xmax,self.ymin,self.ymax,self.noPositionInfo = setupMeshObj(self.modelRoot)
+ self.autocoordinates = False
if self.srcdesConnection:
self.srcdesConnection.clear()
else:
self.srcdesConnection = {}
+
setupItem(self.modelRoot,self.srcdesConnection)
- if not self.positionInfoExist:
+
+ # if not self.positionInfoExist:
+ # autoCoordinates(self.meshEntry,self.srcdesConnection)
+ if not self.noPositionInfo:
+ self.autocoordinates = True
+ #self.xmin,self.xmax,self.ymin,self.ymax,self.autoCordinatepos = autoCoordinates(self.meshEntry,self.srcdesConnection)
+ #print " after ",self.xmin,self.xmax, self.ymin, self.ymax,self.autoCordinatepos
autoCoordinates(self.meshEntry,self.srcdesConnection)
-
+
+ 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
+
+ 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)
@@ -460,7 +488,7 @@ class KineticsWidget(EditorWidgetBase):
item = self.mooseId_GObj[mooseObject]
if (isinstance(item,PoolItem) or isinstance(item,EnzItem) or isinstance(item,MMEnzItem) ):
item.updateColor(color)
-
+ '''
def mooseObjOntoscene(self):
# All the compartments are put first on to the scene \
# Need to do: Check With upi if empty compartments exist
@@ -535,15 +563,116 @@ class KineticsWidget(EditorWidgetBase):
self.setupDisplay(cplxinfo,cplxItem,"cplx")
# compartment's rectangle size is calculated depending on children
- self.comptChilrenBoundingRect()
+ self.comptChildrenBoundingRect()
+ '''
+ def mooseObjOntoscene(self):
+ # All the compartments are put first on to the scene \
+ # Need to do: Check With upi if empty compartments exist
+ self.qGraCompt = {}
+ self.qGraGrp = {}
+ self.mooseId_GObj = {}
+ if self.qGraCompt:
+ self.qGraCompt.clear()
+ else:
+ self.qGraCompt = {}
- def comptChilrenBoundingRect(self):
+ if self.qGraGrp:
+ self.qGraGrp.clear()
+ else:
+ self.qGraGrp = {}
+
+ if self.qGraGrp:
+ self.qGraGrp.clear()
+ else:
+ self.qGraGrp = {}
+
+ if self.mooseId_GObj:
+ self.mooseId_GObj.clear()
+ else:
+ self.mooseId_GObj = {}
+ for k,v in self.objPar.items():
+ if isinstance(moose.element(k),moose.ChemCompt):
+ self.createCompt(k)
+ self.qGraCompt[k]
+
+ elif isinstance(moose.element(k),Neutral):
+ if len(self.meshEntry[k]):
+ if isinstance(moose.element(v), moose.ChemCompt):
+ group_parent = self.qGraCompt[v]
+ elif isinstance(moose.element(v), moose.Neutral):
+ group_parent = self.qGraGrp[v]
+ self.createGroup(k,group_parent)
+ for cmpt_grp,memb in self.meshEntry.items():
+ if len(memb):
+ if isinstance(moose.element(cmpt_grp),moose.ChemCompt):
+ qtGrpparent = self.qGraCompt[cmpt_grp]
+ elif isinstance(moose.element(cmpt_grp), moose.Neutral):
+ qtGrpparent = self.qGraGrp[cmpt_grp]
+ for mclass in ["enzyme","pool","reaction","cplx","function","stimTab"]:
+ self.mObjontoscene(memb,mclass,qtGrpparent)
+
+ self.groupChildrenBoundingRect()
+ # compartment's rectangle size is calculated depending on children
+ self.comptChildrenBoundingRect()
+ def mObjontoscene(self,memb,mclass,qtGrpparent):
+ try:
+ value = memb[mclass]
+ except KeyError:
+ pass
+ else:
+ for mObj in memb[mclass]:
+ minfo = mObj.path+'/info'
+
+ if mObj.className in['Enz',"ZombieEnz"]:
+ mItem = EnzItem(mObj,qtGrpparent)
+
+ elif mObj.className in['MMenz',"ZombieMMenz"]:
+ mItem = MMEnzItem(mObj,qtGrpparent)
+
+ elif isinstance (moose.element(mObj),moose.PoolBase) and mclass != "cplx":
+ #depending on Editor Widget or Run widget pool will be created a PoolItem or PoolItemCircle
+ mItem = self.makePoolItem(mObj,qtGrpparent)
+
+ elif isinstance (moose.element(mObj),moose.ReacBase):
+ mItem = ReacItem(mObj,qtGrpparent)
+
+ elif mclass == "cplx":
+ minfo = (mObj.parent).path+'/info'
+ mItem = CplxItem(mObj,self.mooseId_GObj[element(mObj).parent])
+ self.mooseId_GObj[element(mObj.getId())] = mItem
+ elif mclass == "function":
+ if isinstance(moose.element(mObj.parent),moose.PoolBase):
+ minfo = moose.element(mObj).path+'/info'
+ Af = Annotator(minfo)
+ qtGrpparent = self.mooseId_GObj[element(mObj.parent)]
+ mItem = FuncItem(mObj,qtGrpparent)
+ elif mclass == "stimTab":
+ minfo = mObj.path+'/info'
+ mItem = TableItem(mObj,qtGrpparent)
+ self.mooseId_GObj[element(mObj.getId())] = mItem
+ self.setupDisplay(minfo,mItem,mclass)
+
+ def createGroup(self,key,parent):
+ self.new_GRP = GRPItem(parent,0,0,0,0,key)
+ self.qGraGrp[key] = self.new_GRP
+ self.new_GRP.setRect(20,20,20,20)
+
+ def groupChildrenBoundingRect(self):
+ for k, v in self.qGraGrp.items():
+ grpcolor = moose.Annotator(moose.element(k.path+'/info')).color
+ #Todo: One may need to calculate explicitly the boundary for Group also if there is a cross-group connection, then
+ # childrenBoundrect() will take the QPolygonItem position
+ rectcompt = v.childrenBoundingRect()
+ v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20))
+ v.setPen(QtGui.QPen(Qt.QColor(grpcolor), self.comptPen, Qt.Qt.SolidLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin))
+
+ def comptChildrenBoundingRect(self):
for k, v in self.qGraCompt.items():
# compartment's rectangle size is calculated depending on children
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))
-
+
def createCompt(self,key):
self.new_Compt = ComptItem(self,0,0,0,0,key)
self.qGraCompt[key] = self.new_Compt
@@ -598,8 +727,14 @@ class KineticsWidget(EditorWidgetBase):
'''By this time, model loaded from kkit,cspace,SBML would have info field created and co-ordinates are added
either by autocoordinates (for cspace,SBML(unless it is not saved from moose)) or from kkit
'''
- x = self.defaultScenewidth * float(element(iteminfo).getField('x'))
- y = self.defaultSceneheight *float(element(iteminfo).getField('y'))
+ if moose.Annotator(self.plugin.modelRoot+'/info').modeltype == 'kkit':
+ x = self.defaultScenewidth * float(element(iteminfo).getField('x'))
+ y = self.defaultSceneheight * float(element(iteminfo).getField('y'))
+ #x = x /self.defaultScenewidth
+ #y = y /self.defaultSceneheight
+ else:
+ x = float(element(iteminfo).getField('x'))
+ y = float(element(iteminfo).getField('y'))
return(x,y)
def drawLine_arrow(self, itemignoreZooming=False):
@@ -613,13 +748,13 @@ class KineticsWidget(EditorWidgetBase):
if isinstance(out,tuple):
src = self.mooseId_GObj[inn]
if len(out[0])== 0:
- print inn.className + ' : ' +inn.name+ " doesn't output message"
+ print (inn.className + ' : ' +inn.name+ " doesn't output message")
else:
for items in (items for items in out[0] ):
des = self.mooseId_GObj[element(items[0])]
self.lineCord(src,des,items,itemignoreZooming)
if len(out[1]) == 0:
- print inn.className + ' : ' +inn.name+ " doesn't output message"
+ print (inn.className + ' : ' +inn.name+ " doesn't output message")
else:
for items in (items for items in out[1] ):
des = self.mooseId_GObj[element(items[0])]
@@ -627,9 +762,9 @@ class KineticsWidget(EditorWidgetBase):
elif isinstance(out,list):
if len(out) == 0:
if inn.className == "StimulusTable":
- print inn.name +" doesn't have output"
+ print (inn.name +" doesn't have output")
elif inn.className == "ZombieFunction" or inn.className == "Function":
- print inn.name + " doesn't have sumtotal "
+ print (inn.name + " doesn't have sumtotal ")
else:
src = self.mooseId_GObj[inn]
for items in (items for items in out ):
@@ -640,7 +775,7 @@ class KineticsWidget(EditorWidgetBase):
endtype = type_no[1]
line = 0
if (src == "") and (des == ""):
- print "Source or destination is missing or incorrect"
+ print ("Source or destination is missing or incorrect")
return
srcdes_list = [src,des,endtype,line]
arrow = calcArrow(srcdes_list,itemignoreZooming,self.iconScale)
@@ -653,7 +788,7 @@ class KineticsWidget(EditorWidgetBase):
line = line +1
if type_no[2] > 5:
- print "Higher order reaction will not be displayed"
+ print ("Higher order reaction will not be displayed")
def drawLine(self,srcdes_list,arrow):
src = srcdes_list[0]
@@ -698,7 +833,7 @@ class KineticsWidget(EditorWidgetBase):
#If the item position changes, the corresponding arrow's are calculated
if isinstance(element(mooseObject),ChemCompt):
for k, v in self.qGraCompt.items():
- mesh = mooseObject
+ mesh = moose.element(mooseObject).path
if k.path == mesh:
for rectChilditem in v.childItems():
if isinstance(rectChilditem, KineticsDisplayItem):
@@ -712,6 +847,40 @@ class KineticsWidget(EditorWidgetBase):
j = self.mooseId_GObj[moose.element(i)]
self.updateArrow(j)
self.updateArrow(rectChilditem)
+ elif element(mooseObject).className == 'Neutral':
+ for k,v in self.qGraGrp.items():
+ if k.path == element(mooseObject).path:
+ for grpChilditem in v.childItems():
+ if isinstance(grpChilditem, KineticsDisplayItem):
+ if moose.exists(grpChilditem.mobj.path):
+ iInfo = grpChilditem.mobj.path+'/info'
+ anno = moose.Annotator(iInfo)
+ if moose.Annotator(self.plugin.modelRoot+'/info').modeltype == 'kkit':
+ x = grpChilditem.scenePos().x()/self.defaultScenewidth
+ y = grpChilditem.scenePos().y()/self.defaultSceneheight
+ else:
+ #print "Check for other models at grp level ",grpChilditem.scenePos()
+ x = grpChilditem.scenePos().x()
+ y = grpChilditem.scenePos().y()
+ #print " x and y at 863 ",grpChilditem.scenePos()
+ anno.x = x
+ anno.y = y
+ #print " anno ",anno, anno.x, anno.y
+ if isinstance(moose.element(grpChilditem.mobj.path),PoolBase):
+ t = moose.element(grpChilditem.mobj.path)
+ moose.element(t).children
+ for items in moose.element(t).children:
+ if isinstance(moose.element(items),Function):
+ test = moose.element(items.path+'/x')
+ for i in moose.element(test).neighbors['input']:
+ j = self.mooseId_GObj[moose.element(i)]
+ self.updateArrow(j)
+ self.updateArrow(grpChilditem)
+ # grpcompt = self.qGraCompt[self.objPar[k]]
+ # rectcompt = calculateChildBoundingRect(grpcompt)
+ rectgrp = calculateChildBoundingRect(v)
+ v.setRect(rectgrp.x()-10,rectgrp.y()-10,(rectgrp.width()+20),(rectgrp.height()+20))
+
else:
mobj = self.mooseId_GObj[element(mooseObject)]
self.updateArrow(mobj)
@@ -719,31 +888,50 @@ class KineticsWidget(EditorWidgetBase):
pos = elePath.find('/',1)
l = elePath[0:pos]
linfo = moose.Annotator(l+'/info')
+ if moose.exists(l):
+ #anno = moose.Annotator(linfo)
+ if moose.Annotator(self.plugin.modelRoot+'/info').modeltype == 'kkit':
+ x = mobj.scenePos().x()/self.defaultScenewidth
+ y = mobj.scenePos().y()/self.defaultSceneheight
+ else:
+ #print "Check for other models ",mobj.scenePos()
+ x = mobj.scenePos().x()
+ y = mobj.scenePos().y()
+ #print " x and y at 863 ",mobj.scenePos()
+ # for gk,gv in self.qGraGrp.items():
+ # rectgrp = calculateChildBoundingRect(gv)
+ # grpBoundingRect = gv.boundingRect()
+ # if not grpBoundingRect.contains(rectgrp):
+ # self.updateCompartmentSize(v)
+ # else:
+ # gv.setRect(rectgrp.x()-10,rectgrp.y()-10,(rectgrp.width()+20),(rectgrp.height()+20))
for k, v in self.qGraCompt.items():
#rectcompt = v.childrenBoundingRect()
rectcompt = calculateChildBoundingRect(v)
comptBoundingRect = v.boundingRect()
if not comptBoundingRect.contains(rectcompt):
self.updateCompartmentSize(v)
- '''
- if linfo.modeltype == "new_kkit":
- #if newly built model then compartment is size is fixed for some size.
- comptBoundingRect = v.boundingRect()
- if not comptBoundingRect.contains(rectcompt):
- self.updateCompartmentSize(v)
else:
- #if already built model then compartment size depends on max and min objects
rectcompt = calculateChildBoundingRect(v)
v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20))
- '''
+ pass
+
+ def updateGrpSize(self,compartment):
+ compartmentBoundary = compartment.rect()
+
+ childrenBoundary = calculateChildBoundingRect(compartment)
+ x = childrenBoundary.x()
+ y = childrenBoundary.y()
+ height = childrenBoundary.height()
+ width = childrenBoundary.width()
+ compartment.setRect( x-10
+ , y-10
+ , width + 20
+ , height + 20
+ )
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())
@@ -780,23 +968,6 @@ class KineticsWidget(EditorWidgetBase):
if isinstance(item,CplxItem):
self.updateArrow(item)
- # def deleteSolver(self):
- # print " delete Solver"
- # print "### ",moose.wildcardFind(self.modelRoot+'/data/graph#/#')
- # if moose.wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]'):
- # compt = moose.wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]')
- # print " deletSolver ",
- # # print moose.exists(compt[0].path+'/stoich'), " ksolve ", moose.exists(compt[0].path+'/ksolve')
- # # print "gsolve ", moose.delete( compt[0].path+'/gsolve' )
- # if ( moose.exists( compt[0].path+'/stoich' ) ):
- # #print "delete"
- # moose.delete( compt[0].path+'/stoich' )
- # if ( moose.exists( compt[0].path+'/ksolve' ) ):
- # moose.delete( compt[0].path+'/ksolve' )
- # if ( moose.exists( compt[0].path+'/gsolve' ) ):
- # moose.delete( compt[0].path+'/gsolve' )
- # for x in moose.wildcardFind( self.modelRoot+'/data/graph#/#' ):
- # x.tick = -1
def positionChange1(self,mooseObject):
#If the item position changes, the corresponding arrow's are calculated
if ( (isinstance(element(mooseObject),CubeMesh)) or (isinstance(element(mooseObject),CylMesh))):
@@ -923,58 +1094,6 @@ class kineticRunWidget(KineticsWidget):
for item in self.sceneContainer.items():
if isinstance(item,PoolItemCircle):
item.returnEllispeSize()
-
- # def addSolver(self,solver):
- # print "\t addSolver--------"
- # compt = moose.wildcardFind(self.modelRoot+'/##[ISA=ChemCompt]')
- # comptinfo = moose.Annotator(moose.element(compt[0]).path+'/info')
- # print " $$$$$$$$$$$$$$ ",moose.element(compt[0].path)
- # previousSolver = comptinfo.solver
-
- # print "pre solver from kkit ",previousSolver, solver
- # currentSolver = previousSolver
- # if solver == "Gillespie":
- # currentSolver = "Gillespie"
- # elif solver == "Runge Kutta":
- # currentSolver = "Runge Kutta"
- # elif solver == " Exponential Euler":
- # currentSolver == "Exponential Euler"
-
- # if previousSolver != currentSolver:
- # if ( moose.exists( compt[0].path+'/stoich' ) ):
- # print "1"
- # self.deleteSolver()
- # self.setCompartmentSolver(compt,currentSolver)
- # elif ( moose.exists( compt[0].path+'/stoich' ) ):
- # print "2"
- # self.setCompartmentSolver(compt, currentSolver)
- # comptinfo.solver = currentSolver
- # else:
- # print "3", moose.exists(compt[0].path+'/stoich')
- # if not ( moose.exists( compt[0].path+'/stoich' ) ):
- # self.setCompartmentSolver(compt,currentSolver)
- # for x in moose.wildcardFind( self.modelRoot+'/data/graph#/#' ):
- # x.tick = 18
- # #self.solverStatus()
- # def setCompartmentSolver(self,compt,solver):
- # if solver == 'GSL' or solver == "Runge Kutta":
- # solver = 'gsl'
- # elif solver == 'Gillespie':
- # solver = 'gssa'
- # elif solver == "Exponential Euler":
- # solver = 'ee'
- # print "setCompartmentSolver ",solver
- # if ( solver == 'gsl' ):
- # ksolve = moose.Ksolve( compt[0].path+'/ksolve' )
- # if ( solver == 'gssa' ):
- # ksolve = moose.Gsolve( compt[0].path+'/gsolve' )
- # if (solver!= 'ee'):
- # stoich = moose.Stoich( compt[0].path+'/stoich' )
- # stoich.compartment = compt[0]
- # stoich.ksolve = ksolve
- # stoich.path = compt[0].path+'/##'
- # moose.reinit()
-
if __name__ == "__main__":
app = QtGui.QApplication(sys.argv)
size = QtCore.QSize(1024 ,768)
@@ -988,7 +1107,7 @@ if __name__ == "__main__":
try:
filepath = '../../Demos/Genesis_files/'+modelPath+'.g'
filepath = '/home/harsha/genesis_files/gfile/'+modelPath+'.g'
- print filepath
+ print( "%s" %(filepath))
f = open(filepath, "r")
loadModel(filepath,'/'+modelPath)
@@ -1004,6 +1123,6 @@ if __name__ == "__main__":
except IOError, what:
(errno, strerror) = what
- print "Error number",errno,"(%s)" %strerror
+ print ("Error number",errno,"(%s)" %(strerror))
sys.exit(0)
sys.exit(app.exec_())
diff --git a/plugins/kkitCalcArrow.py b/plugins/kkitCalcArrow.py
index e11ebe3ff29d3110751239f00782dd1f260143ed..4a3128f22159958d6fc6eeb5114a3c4c7c17c2bc 100644
--- a/plugins/kkitCalcArrow.py
+++ b/plugins/kkitCalcArrow.py
@@ -1,6 +1,15 @@
+__author__ = "HarshaRani"
+__credits__ = ["Upi Lab"]
+__license__ = "GPL3"
+__version__ = "1.0.0"
+__maintainer__ = "HarshaRani"
+__email__ = "hrani@ncbs.res.in"
+__status__ = "Development"
+__updated__ = "Jul 27 2017"
+
from PyQt4.QtGui import QPolygonF
from PyQt4.QtCore import QLineF,QPointF
-import math
+from math import sin,cos,atan2,radians
from kkitQGraphics import PoolItem #, ReacItem,EnzItem,CplxItem,ComptItem
''' One to need to pass the source, destination,endtype and order for drawing the arrow between 2 object \
@@ -46,9 +55,9 @@ def calcArrow(srcdes_list,itemignoreZooming,iconScale):
dy = desRect.center().y()- srcRect.center().y()
dx0 = dy
dy0 = -dx
- tetha1 = (math.atan2(dy0,dx0))
- a0 = 4 *(math.cos(tetha1))
- b0 = 4 *(math.sin(tetha1))
+ tetha1 = (atan2(dy0,dx0))
+ a0 = 4 *(cos(tetha1))
+ b0 = 4 *(sin(tetha1))
''' Higher order ( > 4) connectivity will not be done'''
if ((order == 3) or (order == 4)):
a0 = a0*2
@@ -154,9 +163,9 @@ def calcLineRectIntersection(rect, centerLine):
def arrowHead(srcAngle,degree,lineSpoint,iconScale):
''' arrow head is calculated '''
r = 8*iconScale
- delta = math.radians(srcAngle) + math.radians(degree)
- width = math.sin(delta)*r
- height = math.cos(delta)*r
+ delta = radians(srcAngle) + radians(degree)
+ width = sin(delta)*r
+ height = cos(delta)*r
srcXArr = (lineSpoint.x() + width)
srcYArr = (lineSpoint.y() + height)
return srcXArr,srcYArr
diff --git a/plugins/kkitOrdinateUtil.py b/plugins/kkitOrdinateUtil.py
index cdd23bc7d1af6539e7bd077620f78488e023eed3..dd3b967d4b17c4fa94a9ad0e8130b724ed876c6c 100644
--- a/plugins/kkitOrdinateUtil.py
+++ b/plugins/kkitOrdinateUtil.py
@@ -1,5 +1,143 @@
+__author__ = "HarshaRani"
+__credits__ = ["Upi Lab"]
+__license__ = "GPL3"
+__version__ = "1.0.0"
+__maintainer__ = "HarshaRani"
+__email__ = "hrani@ncbs.res.in"
+__status__ = "Development"
+__updated__ = "Oct 18 2017"
+
+'''
+Oct 18: moved some function to kkitUtil
+getxyCord, etc function are added
+'''
+import collections
from moose import *
import numpy as np
+from moose import wildcardFind,element,PoolBase,CplxEnzBase,Annotator,exists
+from networkx.drawing.nx_agraph import graphviz_layout
+import numpy as np
+import networkx as nx
+from kkitUtil import getRandColor,colorCheck,findCompartment, findGroup, findGroup_compt, mooseIsInstance
+from PyQt4.QtGui import QColor
+
+def getxyCord(xcord,ycord,list1):
+ for item in list1:
+ # if isinstance(item,Function):
+ # objInfo = element(item.parent).path+'/info'
+ # else:
+ # objInfo = item.path+'/info'
+ if not isinstance(item,Function):
+ objInfo = item.path+'/info'
+ xcord.append(xyPosition(objInfo,'x'))
+ ycord.append(xyPosition(objInfo,'y'))
+
+def xyPosition(objInfo,xory):
+ try:
+ return(float(element(objInfo).getField(xory)))
+ except ValueError:
+ return (float(0))
+'''
+def mooseIsInstance(melement, classNames):
+ return element(melement).__class__.__name__ in classNames
+
+
+def findCompartment(melement):
+ while not mooseIsInstance(melement, ["CubeMesh", "CyclMesh"]):
+ melement = melement.parent
+ return melement
+
+def findGroup(melement):
+ while not mooseIsInstance(melement, ["Neutral"]):
+ melement = melement.parent
+ return melement
+
+def findGroup_compt(melement):
+ while not (mooseIsInstance(melement, ["Neutral","CubeMesh", "CyclMesh"])):
+ melement = melement.parent
+ return melement
+'''
+def populateMeshEntry(meshEntry,parent,types,obj):
+ #print " parent ",parent, "types ",types, " obj ",obj
+ try:
+ value = meshEntry[element(parent.path)][types]
+ except KeyError:
+ # Key is not present
+ meshEntry[element(parent.path)].update({types :[element(obj)]})
+ else:
+ mlist = meshEntry[element(parent.path)][types]
+ mlist.append(element(obj))
+def updateMeshObj(modelRoot):
+ print " updateMeshObj "
+ meshEntry = {}
+ if meshEntry:
+ meshEntry.clear()
+ else:
+ meshEntry = {}
+
+ objPar = collections.OrderedDict()
+ for compt in wildcardFind(modelRoot+'/##[ISA=ChemCompt]'):
+ groupColor = []
+ try:
+ value = meshEntry[element(compt)]
+ except KeyError:
+ # Compt is not present
+ meshEntry[element(compt)] = {}
+ objPar[element(compt)] = element('/')
+
+ for grp in wildcardFind(compt.path+'/##[TYPE=Neutral]'):
+ test = [x for x in wildcardFind(element(grp).path+'/#') if x.className in ["Pool","Reac","Enz"]]
+ grp_cmpt = findGroup_compt(grp.parent)
+
+ try:
+ value = meshEntry[element(grp)]
+ except KeyError:
+ # Grp is not present
+ meshEntry[element(grp)] = {}
+ objPar[element(grp)] = element(grp_cmpt)
+
+ for compt in wildcardFind(modelRoot+'/##[ISA=ChemCompt]'):
+ for m in wildcardFind(compt.path+'/##[ISA=PoolBase]'):
+ grp_cmpt = findGroup_compt(m)
+ if isinstance(element(grp_cmpt),Neutral):
+ if isinstance(element(m.parent),EnzBase):
+ populateMeshEntry(meshEntry,grp_cmpt,"cplx",m)
+ else:
+ populateMeshEntry(meshEntry,grp_cmpt,"pool",m)
+ else:
+ if isinstance(element(m.parent),EnzBase):
+ populateMeshEntry(meshEntry,compt,"cplx",m)
+ else:
+ populateMeshEntry(meshEntry,compt,"pool",m)
+
+ for r in wildcardFind(compt.path+'/##[ISA=ReacBase]'):
+ rgrp_cmpt = findGroup_compt(r)
+ if isinstance(element(rgrp_cmpt),Neutral):
+ populateMeshEntry(meshEntry,rgrp_cmpt,"reaction",r)
+ else:
+ populateMeshEntry(meshEntry,compt,"reaction",r)
+
+ for e in wildcardFind(compt.path+'/##[ISA=EnzBase]'):
+ egrp_cmpt = findGroup_compt(e)
+ if isinstance(element(egrp_cmpt),Neutral):
+ populateMeshEntry(meshEntry,egrp_cmpt,"enzyme",e)
+ else:
+ populateMeshEntry(meshEntry,compt,"enzyme",e)
+
+ for f in wildcardFind(compt.path+'/##[ISA=Function]'):
+ fgrp_cmpt = findGroup_compt(f)
+ if isinstance(element(fgrp_cmpt),Neutral):
+ populateMeshEntry(meshEntry,fgrp_cmpt,"function",f)
+ else:
+ populateMeshEntry(meshEntry,compt,"function",f)
+
+ for t in wildcardFind(compt.path+'/##[ISA=StimulusTable]'):
+ tgrp_cmpt = findGroup_compt(t)
+ if isinstance(element(tgrp_cmpt),Neutral):
+ populateMeshEntry(meshEntry,tgrp_cmpt,"stimTab",t)
+ else:
+ populateMeshEntry(meshEntry,compt,"stimTab",t)
+ return(objPar,meshEntry)
def setupMeshObj(modelRoot):
''' Setup compartment and its members pool,reaction,enz cplx under self.meshEntry dictionaries \
@@ -7,6 +145,122 @@ def setupMeshObj(modelRoot):
value is key2:list where key2 represents moose object type,list of objects of a perticular type
e.g self.meshEntry[meshEnt] = { 'reaction': reaction_list,'enzyme':enzyme_list,'pool':poollist,'cplx': cplxlist }
'''
+ xmin = 0.0
+ xmax = 1.0
+ ymin = 0.0
+ ymax = 1.0
+ positionInfoExist = True
+ meshEntry = {}
+ if meshEntry:
+ meshEntry.clear()
+ else:
+ meshEntry = {}
+ xcord = []
+ ycord = []
+ n = 1
+ objPar = collections.OrderedDict()
+
+ for compt in wildcardFind(modelRoot+'/##[ISA=ChemCompt]'):
+ groupColor = []
+ try:
+ value = meshEntry[element(compt)]
+ except KeyError:
+ # Compt is not present
+ meshEntry[element(compt)] = {}
+ objPar[element(compt)] = element('/')
+
+ for grp in wildcardFind(compt.path+'/##[TYPE=Neutral]'):
+ test = [x for x in wildcardFind(element(grp).path+'/#') if x.className in ["Pool","Reac","Enz"]]
+ #if len(test) >1:
+ grpinfo = Annotator(element(grp).path+'/info')
+ validatecolor = colorCheck(grpinfo.color,"bg")
+ validatedgrpcolor = str(QColor(validatecolor).name())
+
+ groupColor.append(validatedgrpcolor)
+ grp_cmpt = findGroup_compt(grp.parent)
+
+ try:
+ value = meshEntry[element(grp)]
+ except KeyError:
+ # Grp is not present
+ meshEntry[element(grp)] = {}
+ objPar[element(grp)] = element(grp_cmpt)
+ # if n > 1:
+ # validatecolor = colorCheck(grpinfo.color,"bg")
+ # validatedgrpcolor = str(QColor(validatecolor).name())
+ # if validatedgrpcolor in groupColor:
+ # print " inside "
+ # c = getRandColor()
+ # print " c ",c, c.name()
+ # grpinfo.color = str(c.name())
+ # groupColor.append(str(c.name()))
+ # print " groupColor ",grpinfo,grpinfo.color, groupColor
+ # n =n +1
+ for compt in wildcardFind(modelRoot+'/##[ISA=ChemCompt]'):
+ for m in wildcardFind(compt.path+'/##[ISA=PoolBase]'):
+ grp_cmpt = findGroup_compt(m)
+
+ xcord.append(xyPosition(m.path+'/info','x'))
+ ycord.append(xyPosition(m.path+'/info','y'))
+ if isinstance(element(grp_cmpt),Neutral):
+ if isinstance(element(m.parent),EnzBase):
+ populateMeshEntry(meshEntry,grp_cmpt,"cplx",m)
+ else:
+ populateMeshEntry(meshEntry,grp_cmpt,"pool",m)
+ else:
+ if isinstance(element(m.parent),EnzBase):
+ populateMeshEntry(meshEntry,compt,"cplx",m)
+ else:
+ populateMeshEntry(meshEntry,compt,"pool",m)
+
+ for r in wildcardFind(compt.path+'/##[ISA=ReacBase]'):
+ rgrp_cmpt = findGroup_compt(r)
+ xcord.append(xyPosition(r.path+'/info','x'))
+ ycord.append(xyPosition(r.path+'/info','y'))
+ if isinstance(element(rgrp_cmpt),Neutral):
+ populateMeshEntry(meshEntry,rgrp_cmpt,"reaction",r)
+ else:
+ populateMeshEntry(meshEntry,compt,"reaction",r)
+
+ for e in wildcardFind(compt.path+'/##[ISA=EnzBase]'):
+ egrp_cmpt = findGroup_compt(e)
+ xcord.append(xyPosition(e.path+'/info','x'))
+ ycord.append(xyPosition(e.path+'/info','y'))
+
+ if isinstance(element(egrp_cmpt),Neutral):
+ populateMeshEntry(meshEntry,egrp_cmpt,"enzyme",e)
+ else:
+ populateMeshEntry(meshEntry,compt,"enzyme",e)
+
+ for f in wildcardFind(compt.path+'/##[ISA=Function]'):
+ fgrp_cmpt = findGroup_compt(f)
+ if isinstance(element(fgrp_cmpt),Neutral):
+ populateMeshEntry(meshEntry,fgrp_cmpt,"function",f)
+ else:
+ populateMeshEntry(meshEntry,compt,"function",f)
+
+ for t in wildcardFind(compt.path+'/##[ISA=StimulusTable]'):
+ tgrp_cmpt = findGroup_compt(t)
+ xcord.append(xyPosition(t.path+'/info','x'))
+ ycord.append(xyPosition(t.path+'/info','y'))
+ if isinstance(element(tgrp_cmpt),Neutral):
+ populateMeshEntry(meshEntry,tgrp_cmpt,"stimTab",t)
+ else:
+ populateMeshEntry(meshEntry,compt,"stimTab",t)
+
+ xmin = min(xcord)
+ xmax = max(xcord)
+ ymin = min(ycord)
+ ymax = max(ycord)
+ positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 and len(np.nonzero(ycord)[0]) == 0)
+ return(objPar,meshEntry,xmin,xmax,ymin,ymax,positionInfoExist)
+'''
+def setupMeshObj(modelRoot):
+ # Setup compartment and its members pool,reaction,enz cplx under self.meshEntry dictionaries \
+ # self.meshEntry with "key" as compartment,
+ # value is key2:list where key2 represents moose object type,list of objects of a perticular type
+ # e.g self.meshEntry[meshEnt] = { 'reaction': reaction_list,'enzyme':enzyme_list,'pool':poollist,'cplx': cplxlist }
+
meshEntry = {}
if meshEntry:
meshEntry.clear()
@@ -55,11 +309,11 @@ def setupMeshObj(modelRoot):
def sizeHint(self):
return QtCore.QSize(800,400)
-
+'''
def setupItem(modelPath,cntDict):
- '''This function collects information of what is connected to what. \
- eg. substrate and product connectivity to reaction's and enzyme's \
- sumtotal connectivity to its pool are collected '''
+ # This function collects information of what is connected to what. \
+ # eg. substrate and product connectivity to reaction's and enzyme's \
+ # sumtotal connectivity to its pool are collected
#print " setupItem"
sublist = []
prdlist = []
@@ -80,7 +334,7 @@ def setupItem(modelPath,cntDict):
uniqItem,countuniqItem = countitems(items,'prd')
prdNo = uniqItem
if (len(subNo) == 0 or len(prdNo) == 0):
- print "Substrate Product is empty ",path, " ",items
+ print ("Substrate Product is empty ",path, " ",items)
for prd in uniqItem:
prdlist.append((element(prd),'p',countuniqItem[prd]))
@@ -156,24 +410,26 @@ def xyPosition(objInfo,xory):
def autoCoordinates(meshEntry,srcdesConnection):
- print " kkit Ordinatesutil autoCoordinates "
-
+
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,label='',shape='ellipse',color='',style='filled',fontname='Helvetica',fontsize=12,fontcolor='blue')
+ if memb in ["enzyme"]:
+ for enzObj in find_index(memb,'enzyme'):
+ #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,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_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,label='',shape='circle',color='')
+ #if memb.has_key
+ if memb in ["pool","cplx","reaction"]:
+ for poolObj in find_index(memb,'pool'):
+ #G.add_node(poolObj.path)
+ G.add_node(poolObj.path,label = poolObj.name,shape = 'box',color = '',style = 'filled',fontname = 'Helvetica',fontsize = 9,fontcolor = 'blue')
+ for cplxObj in find_index(memb,'cplx'):
+ G.add_node(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,label='',shape='circle',color='')
for inn,out in srcdesConnection.items():
if (inn.className =='ZombieReac'): arrowcolor = 'green'
@@ -181,22 +437,21 @@ def autoCoordinates(meshEntry,srcdesConnection):
else: arrowcolor = 'blue'
if isinstance(out,tuple):
if len(out[0])== 0:
- print inn.className + ':' +inn.name + " doesn't have input message"
+ print (inn.className + ':' +inn.name + " doesn't have input message")
else:
for items in (items for items in out[0] ):
G.add_edge(element(items[0]).path,inn.path)
if len(out[1]) == 0:
- print inn.className + ':' + inn.name + "doesn't have output mssg"
+ print (inn.className + ':' + inn.name + "doesn't have output mssg")
else:
for items in (items for items in out[1] ):
G.add_edge(inn.path,element(items[0]).path)
elif isinstance(out,list):
if len(out) == 0:
- print "Func pool doesn't have sumtotal"
+ print ("Func pool doesn't have sumtotal")
else:
for items in (items for items in out ):
G.add_edge(element(items[0]).path,inn.path)
-
position = graphviz_layout(G)
xcord, ycord = [],[]
for item in position.items():
@@ -215,9 +470,11 @@ def autoCoordinates(meshEntry,srcdesConnection):
anno = Annotator(item[0]+'/info')
Ax = (xy[0]-xmin)/(xmax-xmin)
Ay = (xy[1]-ymin)/(ymax-ymin)
- anno.x = round(Ax,1)
- anno.y = round(Ay,1)
-
+ #anno.x = round(Ax,1)
+ #anno.y = round(Ay,1)
+ #not roundingoff to max and min the co-ordinates for bigger model would overlay the co-ordinates
+ anno.x = xy[0]
+ anno.y = xy[1]
def find_index(value, key):
""" Value.get(key) to avoid expection which would raise if empty value in dictionary for a given key """
if value.get(key) != None:
diff --git a/plugins/kkitQGraphics.py b/plugins/kkitQGraphics.py
index b0bb4338871e106d8cee4094dc8c187d1ac22454..1f180190a8f133ac5c761c8892121fa10b650a92 100644
--- a/plugins/kkitQGraphics.py
+++ b/plugins/kkitQGraphics.py
@@ -1,3 +1,16 @@
+
+__author__ = "HarshaRani"
+__credits__ = ["Upi Lab"]
+__license__ = "GPL3"
+__version__ = "1.0.0"
+__maintainer__ = "HarshaRani"
+__email__ = "hrani@ncbs.res.in"
+__status__ = "Development"
+__updated__ = "Sep 19 2017"
+
+'''
+sep 19: add GroupItem class
+'''
#import sys
#sys.path.insert(0, '/home/harsha/trunk/gui')
import config
@@ -5,6 +18,7 @@ from PyQt4 import QtGui, QtCore, Qt
from moose import *
from PyQt4.QtGui import QPixmap, QImage, QGraphicsPixmapItem
from constants import *
+from os import path
class KineticsDisplayItem(QtGui.QGraphicsWidget):
"""Base class for display elemenets in kinetics layout"""
@@ -60,7 +74,8 @@ class FuncItem(KineticsDisplayItem):
def __init__(self, mobj, parent):
super(FuncItem, self).__init__(mobj, parent)
self.setFlag(QtGui.QGraphicsItem.ItemIsMovable, True)
- self.funcImage = QImage('icons/classIcon/Function.png').scaled(15,33)
+ iconmap_file = (path.join(config.settings[config.KEY_ICON_DIR], 'classIcon/Function.png'))
+ self.funcImage = QImage(iconmap_file).scaled(15,33)
self.bg = QtGui.QGraphicsRectItem(self)
self.bg.setAcceptHoverEvents(True)
self.gobj = QtGui.QGraphicsPixmapItem(QtGui.QPixmap.fromImage(self.funcImage),self.bg)
@@ -78,7 +93,8 @@ class FuncItem(KineticsDisplayItem):
#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":
+ poolt = ["ZombieBufPool","BufPool","ZombiePool","Pool"]
+ if self.gobj.mobj.parent.className in poolt:
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())
@@ -183,7 +199,9 @@ class PoolItem(KineticsDisplayItem):
#This func will adjust the background color with respect to text size
self.gobj.setText(self.mobj.name)
self.bg.setRect(0, 0, self.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' '), self.gobj.boundingRect().height())
-
+ self.setGeometry(self.pos().x(),self.pos().y(),self.gobj.boundingRect().width()
+ +PoolItem.fontMetrics.width(''),
+ self.gobj.boundingRect().height())
def updateColor(self,bgcolor):
self.bg.setBrush(QtGui.QBrush(QtGui.QColor(bgcolor)))
#pass
@@ -451,6 +469,50 @@ class CplxItem(KineticsDisplayItem):
defaultHeight = CplxItem.defaultHeight*scale
self.gobj.setRect(0,0,defaultWidth,defaultHeight)
+class GRPItem(QtGui.QGraphicsRectItem):
+ #This is used for displaying Grp Item
+ name = GROUP
+ def __init__(self,parent,x,y,w,h,item):
+ self.grpEmitter = QtCore.QObject()
+ QtGui.QGraphicsRectItem.__init__(self,x,y,w,h,parent)
+ self.mobj = item
+ self.setFlag(QtGui.QGraphicsItem.ItemIsMovable, True);
+ self.setFlag(QtGui.QGraphicsItem.ItemIsSelectable)
+ self.setAcceptHoverEvents(True)
+ self.setToolTip(self.mobj.name)
+ QT_VERSION = str(QtCore.QT_VERSION_STR).split('.')
+ QT_MINOR_VERSION = int(QT_VERSION[1])
+ if config.QT_MINOR_VERSION >= 6:
+ self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges, 1)
+
+ # def paint(self, painter=None, option=None, widget = None):
+ # print " self .hasFocus ",self.hasFocus(), " ## ",self.isSelected()
+
+ # if self.isSelected():
+ # drawFocus(painter)
+ # #painter.setPen(QtGui.QPen(QtGui.QPen(QtCore.Qt.black, 1.8,Qt.Qt.DashLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin)))
+ # #painter.drawRect(self.boundingRect())
+
+ # def drawFocusRect(self, painter):
+ # self.focusbrush = QtGui.QBrush()
+ # self.focuspen = QtGui.QPen(QtCore.Qt.DotLine)
+ # self.focuspen.setColor(QtCore.Qt.black)
+ # self.focuspen.setWidthF(1.5)
+ # painter.setBrush(self.focusbrush)
+ # painter.setPen(self.focuspen)
+ # painter.drawRect(self.focusrect)
+
+ def itemChange(self,change,value):
+ #print " itemchange at GRPItem ",change,value
+ if change == QtGui.QGraphicsItem.ItemPositionChange:
+ self.grpEmitter.emit(QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),self.mobj)
+ #if change == QtGui.QGraphicsItem.
+ if change == QtGui.QGraphicsItem.ItemSelectedChange and value == True:
+ #self.setPen(QtGui.QPen(QtGui.QPen(QtCore.Qt.black, 1.8,Qt.Qt.DashLine, Qt.Qt.RoundCap, Qt.Qt.RoundJoin)))
+ #self.drawRect(self.boundingRect())
+ self.grpEmitter.emit(QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),self.mobj)
+
+ return QtGui.QGraphicsItem.itemChange(self,change,value)
class ComptItem(QtGui.QGraphicsRectItem):
name = COMPARTMENT
@@ -479,8 +541,13 @@ class ComptItem(QtGui.QGraphicsRectItem):
self.setFlag(QtGui.QGraphicsItem.ItemIsMovable, True);
self.setFlag(QtGui.QGraphicsItem.ItemIsSelectable)
#self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges, 1)
- if config.QT_MINOR_VERSION >= 6:
- self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges, 1)
+ QT_VERSION = str(QtCore.QT_VERSION_STR).split('.')
+ QT_MINOR_VERSION = int(QT_VERSION[1])
+ if QT_MINOR_VERSION >= 6:
+ #if config.QT_MINOR_VERSION >= 6:
+ self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges, 1)
+ self.setAcceptHoverEvents(True)
+ self.setToolTip(iParent.name)
'''
def hoverEnterEvent(self, event):
self.updateResizeHandles()
diff --git a/plugins/kkitUtil.py b/plugins/kkitUtil.py
index a83a496c320e9e9ddb578e8e4665ad60036c5e73..7185988005fc7c1c15e2795e878870bd1fd9b73f 100644
--- a/plugins/kkitUtil.py
+++ b/plugins/kkitUtil.py
@@ -1,5 +1,17 @@
-from moose import Annotator
-from kkitQGraphics import PoolItem, ReacItem,EnzItem,CplxItem,ComptItem
+__author__ = "HarshaRani"
+__credits__ = ["Upi Lab"]
+__license__ = "GPL3"
+__version__ = "1.0.0"
+__maintainer__ = "HarshaRani"
+__email__ = "hrani@ncbs.res.in"
+__status__ = "Development"
+__updated__ = "Oct 18 2017"
+
+'''
+Oct 18 some of the function moved to this file from kkitOrdinateUtils
+'''
+from moose import Annotator,element
+from kkitQGraphics import PoolItem, ReacItem,EnzItem,CplxItem,GRPItem,ComptItem
from PyQt4 import QtCore,QtGui,QtSvg
from PyQt4.QtGui import QColor
import numpy as np
@@ -119,7 +131,7 @@ def handleCollisions(compartments, moveCallback, layoutPt,margin = 5.0):
if len(compartments) is 0 : return
compartments = sorted(compartments, key = lambda c: c.sceneBoundingRect().center().x())
reference = compartments.pop(0);
- print reference.name
+ print (reference.name)
referenceRect = reference.sceneBoundingRect()
colliders = filter( lambda compartment : referenceRect.intersects(compartment.sceneBoundingRect())
, compartments
@@ -141,10 +153,16 @@ def calculateChildBoundingRect(compt):
''' All the children including pool,reac,enz,polygon(arrow),table '''
if not isinstance(l,QtSvg.QGraphicsSvgItem):
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 (not isinstance(l,GRPItem)):
+ 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())
+ else:
+ xpos.append(l.rect().x())
+ xpos.append(l.boundingRect().bottomRight().x())
+ ypos.append(l.rect().y())
+ ypos.append(l.boundingRect().bottomRight().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():
@@ -162,3 +180,21 @@ def calculateChildBoundingRect(compt):
calculateRectcompt = compt.rect()
return calculateRectcompt
+
+def mooseIsInstance(melement, classNames):
+ return element(melement).__class__.__name__ in classNames
+
+def findCompartment(melement):
+ while not mooseIsInstance(melement, ["CubeMesh", "CyclMesh"]):
+ melement = melement.parent
+ return melement
+
+def findGroup(melement):
+ while not mooseIsInstance(melement, ["Neutral"]):
+ melement = melement.parent
+ return melement
+
+def findGroup_compt(melement):
+ while not (mooseIsInstance(melement, ["Neutral","CubeMesh", "CyclMesh"])):
+ melement = melement.parent
+ return melement
\ No newline at end of file
diff --git a/plugins/kkitViewcontrol.py b/plugins/kkitViewcontrol.py
index c9541743f847dcd8b049ab5aed3440b8845d2210..7d63950455985364a05fb8963a5e521809a71786 100644
--- a/plugins/kkitViewcontrol.py
+++ b/plugins/kkitViewcontrol.py
@@ -1,3 +1,25 @@
+__author__ = "HarshaRani"
+__credits__ = ["Upi Lab"]
+__license__ = "GPL3"
+__version__ = "1.0.0"
+__maintainer__ = "HarshaRani"
+__email__ = "hrani@ncbs.res.in"
+__status__ = "Development"
+__updated__ = "Oct 17 2017"
+
+'''
+Oct 17: If object is moved from one group or compartment to another group or with in same Compartment,
+ then both at moose level (group or compartment path is updated ) and qt level the setParentItem is set
+ -If object is moved to Empty place or not allowed place in the GUI its moved back to origin position
+ -also some clean up when object is just clicked in QsvgItem and v/s clicked and some action done
+ -with Rubber selection if object are moved then group size is updated
+Oct 3 : At mousePressEvent, a clean way of checking on what object mouse press Event happened is checked.
+ This is after group is added where Group Interior and Boundary is checked, with in groupInterior if click in
+ on COMPARTMENT BOUNDARY is clicked then COMPARTMENT_BOUNDARY is return, else top most group object is returned.
+Sep 20: Group related function added
+ -resolveGroupInteriorAndBoundary, findGraphic_groupcompt, graphicsIsInstance
+ -@resolveItem,editorMousePressEvent,editorMouseMoveEvent,editorMouseReleaseEvent checks made for group
+'''
import sys
from modelBuild import *
from constants import *
@@ -66,11 +88,16 @@ class GraphicalView(QtGui.QGraphicsView):
bound = item.rect().adjusted(3,3,-3,-3)
return COMPARTMENT_INTERIOR if bound.contains(item.mapFromScene(position)) else COMPARTMENT_BOUNDARY
+ def resolveGroupInteriorAndBoundary(self, item, position):
+ bound = item.rect().adjusted(3,3,-3,-3)
+ return GROUP_INTERIOR if bound.contains(item.mapFromScene(position)) else GROUP_BOUNDARY
+
def resetState(self):
self.state = { "press" : { "mode" : INVALID
, "item" : None
, "sign" : None
- , "pos" : None
+ , "pos" : None
+ , "scenepos" : None
}
, "move" : { "happened": False
}
@@ -82,129 +109,133 @@ class GraphicalView(QtGui.QGraphicsView):
def resolveItem(self, items, position):
- solution = None
+ csolution = None
+ gsolution = None
+ groupInteriorfound = False
+ groupList = []
+ comptInteriorfound = False
+ comptBoundary = []
+
+ # If clicked , moved and dropped then drop object should not take polygonItem it shd take Goup or compartment
+ #(this is checked is self.state["move"]), else qpolygonItem then deleting the connection b/w 2 objects
+ #move is True the
for item in items:
- # if isinstance(item, QtGui.QGraphicsPixmapItem):
- # return (item, CONNECTOR)
if isinstance(item, QtSvg.QGraphicsSvgItem):
return (item, CONNECTOR)
-
- if isinstance(item, QtGui.QGraphicsPolygonItem):
- return (item, CONNECTION)
+
+ if not self.state["move"]["happened"]:
+ for item in items:
+ if isinstance(item, QtGui.QGraphicsPolygonItem):
+ return (item, CONNECTION)
for item in items:
if hasattr(item, "name"):
- #print(item.name)
if item.name == ITEM:
return (item, ITEM)
+ if item.name == GROUP:
+ gsolution = (item, self.resolveGroupInteriorAndBoundary(item, position))
+ if gsolution[1] == GROUP_BOUNDARY:
+ return gsolution
+ elif gsolution[1] == GROUP_INTERIOR:
+ groupInteriorfound = True
+ groupList.append(gsolution)
+
if item.name == COMPARTMENT:
- solution = (item, self.resolveCompartmentInteriorAndBoundary(item, position))
- if solution is None:
- return (None, EMPTY)
- return solution
+ csolution = (item, self.resolveCompartmentInteriorAndBoundary(item, position))
+ if csolution[1] == COMPARTMENT_BOUNDARY:
+ comptInteriorfound = True
+ comptBoundary.append(csolution)
+
+ if groupInteriorfound:
+ if comptInteriorfound:
+ return comptBoundary[0]
+ else:
+ return groupList[0]
+ else:
+ if csolution is None:
+ return (None, EMPTY)
+ return csolution
+
+ def findGraphic_groupcompt(self,gelement):
+ while not (self.graphicsIsInstance(gelement, ["GRPItem","ComptItem"])):
+ gelement = gelement.parentItem()
+ return gelement
+
+ def graphicsIsInstance(self, gelement, classNames):
+ return gelement.__class__.__name__ in classNames
def editorMousePressEvent(self, event):
- # self.deselectSelections()
- # if self.state["press"]["item"] is not None:
- # self.state["press"]["item"].setSelected(False)
- # self.resetState()
+ self.clickPosition = self.mapToScene(event.pos())
+ (item, itemType) = self.resolveItem(self.items(event.pos()), self.clickPosition)
if event.buttons() == QtCore.Qt.LeftButton:
- self.clickPosition = self.mapToScene(event.pos())
- (item, itemType) = self.resolveItem(self.items(event.pos()), self.clickPosition)
self.state["press"]["mode"] = VALID
self.state["press"]["item"] = item
self.state["press"]["type"] = itemType
self.state["press"]["pos"] = event.pos()
- #If connector exist and if mousePress on Compartment interior,
- # then removing any connect if exist
- if itemType == COMPARTMENT_INTERIOR:
+ if isinstance(item, QtSvg.QGraphicsSvgItem):
+ ##This is kept for reference, so that if object (P,R,E,Tab,Fun) is moved outside the compartment,
+ #then it need to be pull back to original position
+ self.state["press"]["scenepos"] = item.parent().scenePos()
+
+ if itemType == COMPARTMENT_INTERIOR or itemType == GROUP_BOUNDARY or itemType == GROUP_INTERIOR:
self.removeConnector()
+
elif itemType == ITEM:
if not self.move:
self.showConnector(self.state["press"]["item"])
- # self.layoutPt.plugin.mainWindow.objectEditSlot(self.state["press"]["item"].mobj, False)
else:
+ #If right button clicked
self.resetState()
- comptList = []
- for k, v in self.layoutPt.qGraCompt.items():
- comptList.append(v)
- if len(comptList) > 1:
+ if itemType == GROUP_BOUNDARY:
popupmenu = QtGui.QMenu('PopupMenu', self)
- popupmenu.addAction("LinearLayout", lambda : handleCollisions(comptList, moveX, self.layoutPt))
- popupmenu.addAction("VerticalLayout" ,lambda : handleCollisions(comptList, moveMin, self.layoutPt ))
+ popupmenu.addAction("DeleteGroup", lambda : self.deleteGroup(item,self.layoutPt))
+ popupmenu.addAction("CloneGroup" ,lambda : handleCollisions(comptList, moveMin, self.layoutPt ))
popupmenu.exec_(self.mapToGlobal(event.pos()))
+
+ elif itemType == COMPARTMENT_BOUNDARY:
+ if len(list(self.layoutPt.qGraCompt.values())) > 1:
+ popupmenu = QtGui.QMenu('PopupMenu', self)
+ popupmenu.addAction("LinearLayout", lambda : handleCollisions(list(self.layoutPt.qGraCompt.values()), moveX, self.layoutPt))
+ popupmenu.addAction("VerticalLayout" ,lambda : handleCollisions(list(self.layoutPt.qGraCompt.values()), moveMin, self.layoutPt ))
+ popupmenu.exec_(self.mapToGlobal(event.pos()))
-
- def editorMouseMoveEvent(self, event):
+
+ def editorMouseMoveEvent(self,event):
if self.state["press"]["mode"] == INVALID:
self.state["move"]["happened"] = False
return
-
if self.move:
+ #This part of the code is when rubberband selection is done and move option is selected
initial = self.mapToScene(self.state["press"]["pos"])
final = self.mapToScene(event.pos())
displacement = final - initial
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
-
+
self.state["move"]["happened"] = True
itemType = self.state["press"]["type"]
item = self.state["press"]["item"]
-
if itemType == CONNECTOR:
- ''' connecting 2 object is removed and movement is impled'''
actionType = str(item.data(0).toString())
if actionType == "move":
QtGui.QApplication.setOverrideCursor(QtGui.QCursor(QtCore.Qt.CrossCursor))
initial = self.mapToScene(self.state["press"]["pos"])
- #initial = item.parent().pos()
final = self.mapToScene(event.pos())
displacement = final-initial
- if isinstance(item.parent(),KineticsDisplayItem):
- itemPath = item.parent().mobj.path
- if moose.exists(itemPath):
- iInfo = itemPath+'/info'
- anno = moose.Annotator(iInfo)
- modelAnno = moose.Annotator(self.modelRoot+'/info')
- x = item.parent().scenePos().x()/self.layoutPt.defaultScenewidth
- y = item.parent().scenePos().y()/self.layoutPt.defaultSceneheight
- anno.x = x
- anno.y = y
- '''
- 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
- print " kvc CONNECTOR ",item.parent().mobj, displacement.x(), " y ",displacement.y()
- print "scenePos CONNECTOR",item.parent().scenePos().x(),item.parent().scenePos().y(),
- print "dive x ",item.parent().scenePos().x()/1000, " y ",item.parent().scenePos().y()/500
- #item.parent().update()
- #self.updateScale(1)
- x = item.parent().scenePos().x()/1000
- y = item.parent().scenePos().y()/500
- 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(),CplxItem):
- self.removeConnector()
- item.parent().moveBy(displacement.x(), displacement.y())
- if isinstance(item.parent(),PoolItem):
- for funcItem in item.parent().childItems():
- if isinstance(funcItem,FuncItem):
- self.layoutPt.updateArrow(funcItem)
-
+ self.removeConnector()
+ item.parent().moveBy(displacement.x(), displacement.y())
+ #self.layoutPt.updateArrow(item.parent())
+ if isinstance(item.parent(),PoolItem):
+ for funcItem in item.parent().childItems():
+ if isinstance(funcItem,FuncItem):
+ self.layoutPt.updateArrow(funcItem)
self.state["press"]["pos"] = event.pos()
self.layoutPt.positionChange(item.parent().mobj)
- if actionType == "clone":
+ elif actionType == "clone":
pixmap = QtGui.QPixmap(24, 24)
pixmap.fill(QtCore.Qt.transparent)
painter = QtGui.QPainter()
@@ -216,13 +247,12 @@ class GraphicalView(QtGui.QGraphicsView):
painter.drawLine(12,7,12,17)
painter.drawLine(7,12,17,12)
painter.end()
- #self.setCursor(QtGui.QCursor(pixmap))
QtGui.QApplication.setOverrideCursor(QtGui.QCursor(pixmap))
if itemType == ITEM:
self.drawExpectedConnection(event)
- if itemType == COMPARTMENT_BOUNDARY:
+ if itemType == COMPARTMENT_BOUNDARY or itemType == GROUP_BOUNDARY:
initial = self.mapToScene(self.state["press"]["pos"])
final = self.mapToScene(event.pos())
displacement = final - initial
@@ -230,7 +260,7 @@ class GraphicalView(QtGui.QGraphicsView):
self.layoutPt.positionChange(item.mobj.path)
self.state["press"]["pos"] = event.pos()
- if itemType == COMPARTMENT_INTERIOR:
+ if itemType == COMPARTMENT_INTERIOR or itemType == GROUP_INTERIOR:
if self.customrubberBand == None:
self.customrubberBand = QtGui.QRubberBand(QtGui.QRubberBand.Rectangle,self)
self.customrubberBand.show()
@@ -252,20 +282,11 @@ class GraphicalView(QtGui.QGraphicsView):
self.customrubberBand.setGeometry(QtCore.QRect(QtCore.QPoint(x0, y0), QtCore.QSize(abs(displacement.x()), abs(displacement.y()))))
-
- # if itemType == COMPARTMENT:
- # rubberband selection
-
- # if itemType == COMPARTMENT_BOUNDARY:
-
- # if itemType == ITEM:
- # dragging the item
-
- def editorMouseReleaseEvent(self, event):
+ def editorMouseReleaseEvent(self,event):
if self.move:
self.move = False
self.setCursor(Qt.Qt.ArrowCursor)
-
+
if self.state["press"]["mode"] == INVALID:
self.state["release"]["mode"] = INVALID
self.resetState()
@@ -287,8 +308,10 @@ class GraphicalView(QtGui.QGraphicsView):
l = self.modelRoot
if self.modelRoot.find('/',1) > 0:
l = self.modelRoot[0:self.modelRoot.find('/',1)]
-
- linfo = moose.Annotator(l+'/model/info')
+ linfo = moose.Annotator(l+'/info')
+ for k,v in self.layoutPt.qGraGrp.items():
+ rectgrp = calculateChildBoundingRect(v)
+ v.setRect(rectgrp.x()-10,rectgrp.y()-10,(rectgrp.width()+20),(rectgrp.height()+20))
for k, v in self.layoutPt.qGraCompt.items():
rectcompt = v.childrenBoundingRect()
if linfo.modeltype == "new_kkit":
@@ -302,6 +325,7 @@ class GraphicalView(QtGui.QGraphicsView):
v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20))
else:
+ #When group is moved then compartment need to be update which is done here
if isinstance(self.state["release"]["item"], KineticsDisplayItem):
if not moose.element(self.state["press"]["item"].mobj) == moose.element(self.state["release"]["item"].mobj):
self.populate_srcdes( self.state["press"]["item"].mobj
@@ -311,13 +335,69 @@ class GraphicalView(QtGui.QGraphicsView):
pass
self.removeExpectedConnection()
self.removeConnector()
- self.move = False
- if clickedItemType == CONNECTOR:
+ self.move = False
+ elif clickedItemType == CONNECTOR:
actionType = str(self.state["press"]["item"].data(0).toString())
-
-
+ pressItem = self.state["press"]["item"]
+
if actionType == "move":
QtGui.QApplication.setOverrideCursor(QtGui.QCursor(Qt.Qt.ArrowCursor))
+ #If any case, move is not valide need to move back the object to original position is store and calculation
+ initscenepos = self.state["press"]["scenepos"]
+ finialscenepos = pressItem.parent().scenePos()
+ xx = finialscenepos.x()-initscenepos.x()
+ yy = finialscenepos.y()-initscenepos.y()
+
+ if itemType == EMPTY:
+ pressItem.parent().moveBy(-xx,-yy)
+ self.layoutPt.updateArrow(pressItem.parent())
+ QtGui.QMessageBox.warning(None,'Could not move the object', "The object can't be moved to empty space")
+ else:
+ if isinstance(self.state["press"]["item"], Qt.QGraphicsSvgItem):
+ pressedItem = self.state["press"]["item"]
+ releaseItem = self.state["release"]["item"]
+ sgrp = findGroup(pressItem.parent().mobj)
+ scmpt = findCompartment(pressItem.parent().mobj)
+ dgrp = findGroup(releaseItem.mobj)
+ dcmpt = findCompartment(releaseItem.mobj)
+ if isinstance(dgrp,Neutral):
+ # This is obj moved from group to
+ # - another group
+ # - into compartment
+ if sgrp.path != dgrp.path:
+ if scmpt.volume == dcmpt.volume:
+ #With in same compartment but different group
+ moose.move(pressItem.parent().mobj,dgrp)
+ lKey = self.layoutPt.qGraGrp[dgrp]
+ pressItem.parent().setParentItem(lKey)
+ self.layoutPt.positionChange(sgrp)
+ self.layoutPt.positionChange(dgrp)
+ else:
+ #If object is tried to move to diff compartment,
+ # then object will be pulled back to origin position which it was moved from
+ pressItem.parent().moveBy(-xx,-yy)
+ self.layoutPt.updateArrow(pressItem.parent())
+ QtGui.QMessageBox.warning(None,'Could not move the object', "The object can't be moved to empty space")
+ elif isinstance(dcmpt,CubeMesh):
+ # This is obj moved from group into compartment
+ if scmpt.path != dcmpt.path:
+ if scmpt.volume == dcmpt.volume:
+ moose.move(pressItem.parent().mobj,dcmpt)
+ lKey = self.layoutPt.qGraCompt[dcmpt]
+ pressItem.parent().setParentItem(lKey)
+ self.layoutPt.positionChange(sgrp)
+ self.layoutPt.positionChange(dgrp)
+ else:
+ #If object is tried to move to diff compartment,
+ # then object will be pulled back to origin position which it was moved from
+ pressItem.parent().moveBy(-xx,-yy)
+ self.layoutPt.updateArrow(pressItem.parent())
+ QtGui.QMessageBox.warning(None,'Could not move the object', "The object can't be moved to empty space")
+ else:
+ print " Check what moved when! does it reaches this condition"
+
+ self.layoutPt.positionChange(item.mobj)
+ self.updateScale(self.iconScale)
if actionType == "delete":
self.removeConnector()
@@ -346,7 +426,12 @@ class GraphicalView(QtGui.QGraphicsView):
elif actionType == "plot":
element = moose.element(item.parent().mobj.path)
if isinstance (element,moose.PoolBase):
- self.graph = moose.element(self.modelRoot+'/data/graph_0')
+ if moose.exists(self.modelRoot+'/data/graph_0'):
+ self.graph = moose.element(self.modelRoot+'/data/graph_0')
+ else:
+ moose.Neutral(self.modelRoot+'/data')
+ moose.Neutral(self.modelRoot+'/data/graph_0')
+ self.graph = moose.element(self.modelRoot+'/data/graph_0')
tablePath = utils.create_table_path(moose.element(self.modelRoot), self.graph, element, "Conc")
table = utils.create_table(tablePath, element, "Conc","Table2")
self.layoutPt.plugin.view.getCentralWidget().plotWidgetContainer.plotAllData()
@@ -360,12 +445,16 @@ class GraphicalView(QtGui.QGraphicsView):
posWrtComp = self.mapToScene(event.pos())
itemAtView = self.sceneContainerPt.itemAt(self.mapToScene(event.pos()))
self.removeConnector()
- if isinstance(itemAtView,ComptItem):
+ if isinstance(itemAtView,ComptItem) or isinstance(itemAtView, GRPItem):
#Solver should be deleted
## if there is change in 'Topology' of the model
## or if copy has to made then oject should be in unZombify mode
deleteSolver(self.modelRoot)
- lKey = [key for key, value in self.layoutPt.qGraCompt.iteritems() if value == itemAtView][0]
+ #As name is suggesting, if item is Compartment, then search in qGraCompt and if group then qGraGrp
+ if isinstance(itemAtView,ComptItem):
+ lKey = [key for key, value in self.layoutPt.qGraCompt.iteritems() if value == itemAtView][0]
+ if isinstance (itemAtView, GRPItem):
+ lKey = [key for key, value in self.layoutPt.qGraGrp.iteritems() if value == itemAtView][0]
iR = 0
iP = 0
t = moose.element(cloneObj.parent().mobj)
@@ -374,9 +463,7 @@ class GraphicalView(QtGui.QGraphicsView):
retValue = self.objExist(lKey.path,name,iP)
if retValue != None:
name += retValue
-
pmooseCp = moose.copy(t,lKey.path,name,1)
- #if moose.copy failed then check for path != '/'
if pmooseCp.path != '/':
ct = moose.element(pmooseCp)
concInit = pmooseCp.concInit[0]
@@ -401,7 +488,6 @@ class GraphicalView(QtGui.QGraphicsView):
rmooseCp = moose.copy(t,lKey.path,name,1)
if rmooseCp.path != '/':
ct = moose.element(rmooseCp)
- #itemAtView = self.state["release"]["item"]
reacObj = moose.element(ct)
reacinfo = moose.Annotator(reacObj.path+'/info')
qGItem = ReacItem(reacObj,itemAtView)
@@ -409,26 +495,27 @@ class GraphicalView(QtGui.QGraphicsView):
posWrtComp = self.mapToScene(event.pos())
qGItem.setDisplayProperties(posWrtComp.x(),posWrtComp.y(),"white", "white")
self.emit(QtCore.SIGNAL("dropped"),reacObj)
-
self.updateScale(self.iconScale)
-
else:
if itemAtView == None:
QtGui.QMessageBox.information(None,'Dropping Not possible ','Dropping not allowed outside the compartment',QtGui.QMessageBox.Ok)
else:
srcdesString = ((self.state["release"]["item"]).mobj).className
QtGui.QMessageBox.information(None,'Dropping Not possible','Dropping on \'{srcdesString}\' not allowed'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok)
+
if clickedItemType == CONNECTION:
popupmenu = QtGui.QMenu('PopupMenu', self)
popupmenu.addAction("Delete", lambda : self.deleteConnection(item))
popupmenu.exec_(self.mapToGlobal(event.pos()))
- if clickedItemType == COMPARTMENT_BOUNDARY:
- if not self.state["move"]["happened"]:
- self.layoutPt.plugin.mainWindow.objectEditSlot(self.state["press"]["item"].mobj, True)
- self.resetState()
+ if clickedItemType == COMPARTMENT_BOUNDARY or clickedItemType == GROUP_BOUNDARY:
+ if item != None:
+ item.setSelected(True)
+ if not self.state["move"]["happened"]:
+ self.layoutPt.plugin.mainWindow.objectEditSlot(self.state["press"]["item"].mobj, True)
+ self.resetState()
- if clickedItemType == COMPARTMENT_INTERIOR:
+ if clickedItemType == COMPARTMENT_INTERIOR or clickedItemType == GROUP_INTERIOR:
if self.state["move"]["happened"]:
startingPosition = self.state["press"]["pos"]
endingPosition = event.pos()
@@ -444,36 +531,30 @@ class GraphicalView(QtGui.QGraphicsView):
if displacement.y() < 0 :
y0,y1= y1,y0
- #print "kkitview COMPARTMENT_INTERIOR",x0,y0
self.selectedItems = selectedItems = self.items(x0,y0,abs(displacement.x()), abs(displacement.y()))
- # print("Rect => ", self.customrubberBand.rect())
- # selectedItems = self.items(self.mapToScene(self.customrubberBand.rect()).boundingRect())
self.selectSelections(selectedItems)
for item in selectedItems:
if isinstance(item, KineticsDisplayItem) and not isinstance(item,ComptItem):
item.setSelected(True)
- #print("Rubberband Selections => ", self.selections)
- self.customrubberBand.hide()
- self.customrubberBand = None
+ if self.customrubberBand != None:
+ self.customrubberBand.hide()
+ self.customrubberBand = None
popupmenu = QtGui.QMenu('PopupMenu', self)
popupmenu.addAction("Delete", lambda: self.deleteSelections(x0,y0,x1,y1))
popupmenu.addAction("Zoom", lambda: self.zoomSelections(x0,y0,x1,y1))
popupmenu.addAction("Move", lambda: self.moveSelections())
- popupmenu.exec_(self.mapToGlobal(event.pos()))
- # self.delete = QtGui.QAction(self.tr('delete'), self)
- # self.connect(self.delete, QtCore.SIGNAL('triggered()'), self.deleteItems)
- # self.zoom = QtGui.QAction(self.tr('zoom'), self)
- # self.connect(self.zoom, QtCore.SIGNAL('triggered()'), self.zoomItem)
- # self.move = QtGui.QAction(self.tr('move'), self)
- # self.connect(self.move, QtCore.SIGNAL('triggered()'), self.moveItem)
-
-
-
-
- # else:
- # self.layoutPt.plugin.mainWindow.objectEditSlot(self.state["press"]["item"].mobj, True)
+ popupmenu.exec_(self.mapToGlobal(event.pos()))
self.resetState()
+
+ def deleteGroup(self,item,layoutPt):
+ key = [k for k,v in self.layoutPt.qGraGrp.items() if v == item]
+ if key[0] in self.layoutPt.qGraGrp:
+ self.layoutPt.qGraGrp.pop(key[0])
+ self.groupItemlist1 = item.childItems()
+ self.groupItemlist = [ i for i in self.groupItemlist1 if not isinstance(i,QtGui.QGraphicsPolygonItem)]
+ self.deleteObj(self.groupItemlist)
+ self.deleteItem(item)
def drawExpectedConnection(self, event):
self.connectionSource = self.state["press"]["item"]
@@ -497,30 +578,7 @@ class GraphicalView(QtGui.QGraphicsView):
, destinationPoint.y()
)
- '''
- print " drawExpectedConnection ()() ",self.state["item"]["press"].mobj
- sourcePoint = self.connectionSource.mapToScene(
- self.connectionSource.boundingRect().center()
- )
- destinationPoint = self.mapToScene(event.pos())
- if self.expectedConnection is None:
- self.expectedConnection = QGraphicsLineItem( sourcePoint.x()
- , sourcePoint.y()
- , destinationPoint.x()
- , destinationPoint.y()
- )
- self.expectedConnection.setPen(QPen(Qt.Qt.DashLine))
-
- self.sceneContainerPt.addItem(self.expectedConnection)
- else:
- self.expectedConnection.setLine( sourcePoint.x()
- , sourcePoint.y()
- , destinationPoint.x()
- , destinationPoint.y()
- )
- '''
def removeExpectedConnection(self):
- #print("removeExpectedConnection")
self.sceneContainerPt.removeItem(self.expectedConnection)
self.expectedConnection = None
self.connectionSource = None
@@ -531,18 +589,9 @@ class GraphicalView(QtGui.QGraphicsView):
if k is not None:
self.sceneContainerPt.removeItem(k)
self.connectorlist[l] = None
- '''
- if self.connectionSign is not None:
- # self.sceneContainerPt.removeItem(self.connectionSign)
- # self.connectionSign = None
- '''
except:
#print("Exception received!")
pass
- # if self.connectionSign is not None:
- # print "self.connectionSign ",self.connectionSign
- # self.sceneContainerPt.removeItem(self.connectionSign)
- # self.connectionSign = None
def showConnector(self, item):
self.removeConnector()
@@ -700,39 +749,9 @@ class GraphicalView(QtGui.QGraphicsView):
des = [j for j in destination if isinstance(j,KineticsDisplayItem)]
if len(des):
self.populate_srcdes(src.mobj,des[0].mobj)
- #print " pop", self.layoutPt.srcdesConnection()
self.setCursor(Qt.Qt.ArrowCursor)
QtGui.QGraphicsView.mouseReleaseEvent(self, event)
- '''if(self.customrubberBand):
- self.customrubberBand.hide()
- self.customrubberBand = 0
- if event.button() == QtCore.Qt.LeftButton and self.itemSelected == False :
- self.endingPos = event.pos()
- self.endScenepos = self.mapToScene(self.endingPos)
- self.rubberbandWidth = (self.endScenepos.x()-self.startScenepos.x())
- self.rubberbandHeight = (self.endScenepos.y()-self.startScenepos.y())
- selecteditems = self.sceneContainerPt.selectedItems()
- #print "selecteditems ",selecteditems
- if self.rubberbandWidth != 0 and self.rubberbandHeight != 0 and len(selecteditems) != 0 :
- self.showpopupmenu = True
- '''
- #self.itemSelected = False
- '''
- if self.showpopupmenu:
- popupmenu = QtGui.QMenu('PopupMenu', self)
- self.delete = QtGui.QAction(self.tr('delete'), self)
- self.connect(self.delete, QtCore.SIGNAL('triggered()'), self.deleteItems)
- self.zoom = QtGui.QAction(self.tr('zoom'), self)
- self.connect(self.zoom, QtCore.SIGNAL('triggered()'), self.zoomItem)
- self.move = QtGui.QAction(self.tr('move'), self)
- self.connect(self.move, QtCore.SIGNAL('triggered()'), self.moveItem)
- popupmenu.addAction(self.delete)
- popupmenu.addAction(self.zoom)
- popupmenu.addAction(self.move)
- popupmenu.exec_(event.globalPos())
- self.showpopupmenu = False
- '''
-
+
def updateItemTransformationMode(self, on):
for v in self.sceneContainerPt.items():
#v.setFlag(QtGui.QGraphicsItem.ItemIgnoresTransformations,on)
@@ -746,7 +765,7 @@ class GraphicalView(QtGui.QGraphicsView):
if (key == Qt.Qt.Key_A and (event.modifiers() & Qt.Qt.ShiftModifier)): # 'A' fits the view to iconScale factor
itemignoreZooming = False
self.updateItemTransformationMode(itemignoreZooming)
- self.fitInView(self.sceneContainerPt.itemsBoundingRect().x()-10,self.sceneContainerPt.itemsBoundingRect().y()-10,self.sceneContainerPt.itemsBoundingRect().width()+20,self.sceneContainerPt.itemsBoundingRect().height()+20,Qt.Qt.IgnoreAspectRatio)
+ #self.fitInView(self.sceneContainerPt.itemsBoundingRect().x()-10,self.sceneContainerPt.itemsBoundingRect().y()-10,self.sceneContainerPt.itemsBoundingRect().width()+20,self.sceneContainerPt.itemsBoundingRect().height()+20,Qt.Qt.IgnoreAspectRatio)
self.layoutPt.drawLine_arrow(itemignoreZooming=False)
elif (key == Qt.Qt.Key_Less or key == Qt.Qt.Key_Minus):# and (event.modifiers() & Qt.Qt.ShiftModifier)): # '<' key. zooms-in to iconScale factor
@@ -764,6 +783,7 @@ class GraphicalView(QtGui.QGraphicsView):
self.scale(1/1.1,1/1.1)
elif (key == Qt.Qt.Key_A): # 'a' fits the view to initial value where iconscale=1
+ self.iconscale = 1
self.updateScale( 1 )
self.fitInView(self.sceneContainerPt.itemsBoundingRect().x()-10,self.sceneContainerPt.itemsBoundingRect().y()-10,self.sceneContainerPt.itemsBoundingRect().width()+20,self.sceneContainerPt.itemsBoundingRect().height()+20,Qt.Qt.IgnoreAspectRatio)
@@ -771,10 +791,8 @@ class GraphicalView(QtGui.QGraphicsView):
for item in self.sceneContainerPt.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()
+ xpos = item.pos().x()
+ ypos = item.pos().y()
if isinstance(item,ReacItem) or isinstance(item,EnzItem) or isinstance(item,MMEnzItem):
item.setGeometry(xpos,ypos,
item.gobj.boundingRect().width(),
@@ -790,23 +808,14 @@ class GraphicalView(QtGui.QGraphicsView):
item.bg.setRect(0, 0, item.gobj.boundingRect().width()+PoolItem.fontMetrics.width(' '), item.gobj.boundingRect().height())
self.layoutPt.drawLine_arrow(itemignoreZooming=False)
- self.layoutPt.comptChilrenBoundingRect()
- #compartment width is resize according apart from calculating boundingRect
- # for k, v in self.layoutPt.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))
-
+ self.layoutPt.comptChildrenBoundingRect()
+
def moveSelections(self):
self.setCursor(Qt.Qt.CrossCursor)
self.move = True
return
def GrVfitinView(self):
- #print " here in GrVfitinView"
itemignoreZooming = False
self.layoutPt.updateItemTransformationMode(itemignoreZooming)
self.fitInView(self.sceneContainerPt.itemsBoundingRect().x()-10,self.sceneContainerPt.itemsBoundingRect().y()-10,self.sceneContainerPt.itemsBoundingRect().width()+20,self.sceneContainerPt.itemsBoundingRect().height()+20,Qt.Qt.IgnoreAspectRatio)
@@ -814,51 +823,40 @@ class GraphicalView(QtGui.QGraphicsView):
def deleteSelections(self,x0,y0,x1,y1):
if( x1-x0 > 0 and y1-y0 >0):
- self.rubberbandlist = self.sceneContainerPt.items(self.mapToScene(QtCore.QRect(x0, y0, x1 - x0, y1 - y0)).boundingRect(), Qt.Qt.IntersectsItemShape)
- for unselectitem in self.rubberbandlist:
+ # self.rubberbandlist = self.sceneContainerPt.items(self.mapToScene(QtCore.QRect(x0, y0, x1 - x0, y1 - y0)).boundingRect(), Qt.Qt.IntersectsItemShape)
+ # for unselectitem in self.rubberbandlist:
+ self.rubberbandlist_qpolygon = []
+ for unselectitem in self.rubberbandlist_qpolygon:
if unselectitem.isSelected() == True:
unselectitem.setSelected(0)
+ self.rubberbandlist_qpolygon = self.sceneContainerPt.items(self.mapToScene(QtCore.QRect(x0, y0, x1 - x0, y1 - y0)).boundingRect(), Qt.Qt.IntersectsItemShape)
self.deleteObj(self.rubberbandlist)
- # deleteSolver(self.layoutPt.modelRoot)
- # for item in (qgraphicsitem for qgraphicsitem in self.rubberbandlist):
- # #First Loop to remove all the enz b'cos if parent (which is a Pool) is removed,
- # #then it will created problem at qgraphicalitem not having parent.
- # #So first delete enz and then delete pool
- # if isinstance(item,MMEnzItem) or isinstance(item,EnzItem) or isinstance(item,CplxItem):
- # self.deleteItem(item)
- # for item in (qgraphicsitem for qgraphicsitem in self.rubberbandlist):
- # if not (isinstance(item,MMEnzItem) or isinstance(item,EnzItem) or isinstance(item,CplxItem)):
- # if isinstance(item,PoolItem):
- # plot = moose.wildcardFind(self.layoutPt.modelRoot+'/data/graph#/#')
- # for p in plot:
- # if len(p.neighbors['requestOut']):
- # if item.mobj.path == moose.element(p.neighbors['requestOut'][0]).path:
- # p.tick = -1
- # moose.delete(p)
- # self.layoutPt.plugin.view.getCentralWidget().plotWidgetContainer.plotAllData()
- # self.deleteItem(item)
self.selections = []
+
def deleteObj(self,item):
self.rubberbandlist = item
deleteSolver(self.layoutPt.modelRoot)
- for item in (qgraphicsitem for qgraphicsitem in self.rubberbandlist):
+ self.Enz_cplxlist = [ i for i in self.rubberbandlist if (isinstance(i,MMEnzItem) or isinstance(i,EnzItem) or isinstance(i,CplxItem) )]
+ self.PFRSlist = [ i for i in self.rubberbandlist if (isinstance(i,PoolItem) or isinstance(i,TableItem) or isinstance(i,ReacItem) or isinstance(i,FuncItem) )]
+ self.grp = [ i for i in self.rubberbandlist if isinstance(i,GRPItem)]
+ for item in self.Enz_cplxlist:
#First Loop to remove all the enz b'cos if parent (which is a Pool) is removed,
#then it will created problem at qgraphicalitem not having parent.
#So first delete enz and then delete pool
- if isinstance(item,MMEnzItem) or isinstance(item,EnzItem) or isinstance(item,CplxItem):
- self.deleteItem(item)
- for item in (qgraphicsitem for qgraphicsitem in self.rubberbandlist):
- if not (isinstance(item,MMEnzItem) or isinstance(item,EnzItem) or isinstance(item,CplxItem)):
- if isinstance(item,PoolItem):
- plot = moose.wildcardFind(self.layoutPt.modelRoot+'/data/graph#/#')
- for p in plot:
- if len(p.neighbors['requestOut']):
- if item.mobj.path == moose.element(p.neighbors['requestOut'][0]).path:
- p.tick = -1
- moose.delete(p)
- self.layoutPt.plugin.view.getCentralWidget().plotWidgetContainer.plotAllData()
- self.deleteItem(item)
-
+ self.deleteItem(item)
+ for item in self.PFRSlist:
+ if isinstance(item,PoolItem) or isinstance(item,BufPool):
+ plot = moose.wildcardFind(self.layoutPt.modelRoot+'/data/graph#/#')
+ for p in plot:
+ if len(p.neighbors['requestOut']):
+ if item.mobj.path == moose.element(p.neighbors['requestOut'][0]).path:
+ p.tick = -1
+ moose.delete(p)
+ self.layoutPt.plugin.view.getCentralWidget().plotWidgetContainer.plotAllData()
+ self.deleteItem(item)
+ for item in self.grp:
+ self.deleteItem(item)
+
def deleteObject2line(self,qpolygonline,src,des,endt):
object2lineInfo = self.layoutPt.object2line[des]
if len(object2lineInfo) == 1:
@@ -866,7 +864,7 @@ class GraphicalView(QtGui.QGraphicsView):
if polygon == qpolygonline and objdes == src and endtype == endt:
del(self.layoutPt.object2line[des])
else:
- print " check this condition when is len is single and else condition",qpolygonline, objdes,endtype
+ print( " check this condition when is len is single and else condition",qpolygonline, objdes,endtype)
else:
n = 0
for polygon,objdes,endtype,numL in object2lineInfo:
@@ -1003,26 +1001,13 @@ class GraphicalView(QtGui.QGraphicsView):
#delete Items
self.layoutPt.plugin.mainWindow.objectEditSlot('/', False)
- if isinstance(item,KineticsDisplayItem):
+ if isinstance(item,KineticsDisplayItem) or isinstance(item,GRPItem):
if moose.exists(item.mobj.path):
- # if isinstance(item.mobj,Function):
- # print " inside the function"
- # for items in moose.element(item.mobj.path).children:
- # print items
if isinstance(item,PoolItem) or isinstance(item,BufPool):
# pool is item is removed, then check is made if its a parent to any
# enz if 'yes', then enz and its connection are removed before
# removing Pool
for items in moose.element(item.mobj.path).children:
- # if isinstance(moose.element(items), Function):
- # gItem = self.layoutPt.mooseId_GObj[moose.element(items)]
- # for l in self.layoutPt.object2line[gItem]:
- # sceneItems = self.sceneContainerPt.items()
- # if l[0] in sceneItems:
- # #deleting the connection which is connected to Enz
- # self.sceneContainerPt.removeItem(l[0])
- # moose.delete(items)
- # self.sceneContainerPt.removeItem(gItem)
if isinstance(moose.element(items), EnzBase):
gItem = self.layoutPt.mooseId_GObj[moose.element(items)]
for l in self.layoutPt.object2line[gItem]:
@@ -1059,7 +1044,6 @@ class GraphicalView(QtGui.QGraphicsView):
def zoomSelections(self, x0, y0, x1, y1):
p0 = self.mapToScene(x0, y0)
p1 = self.mapToScene(x1, y1)
- #print QtCore.QRectF(p0, p1)
self.fitInView(QtCore.QRectF(p0, p1), Qt.Qt.KeepAspectRatio)
self.deselectSelections()
return
@@ -1119,7 +1103,6 @@ class GraphicalView(QtGui.QGraphicsView):
founds, foundp = False,False
if isinstance(moose.element(des),EnzBase):
- print moose.element(des).neighbors["subOut"]
if len(moose.element(des).neighbors["subOut"]) > 0:
founds = True
@@ -1195,10 +1178,6 @@ class GraphicalView(QtGui.QGraphicsView):
elif founds:
srcdesString = desClass+' is already connected as '+'\'Substrate\''+' to '+srcClass +' \n \nIf you wish to connect this object then first delete the exist connection'
QtGui.QMessageBox.information(None,'Connection Not possible','{srcdesString}'.format(srcdesString = srcdesString),QtGui.QMessageBox.Ok)
- # elif( isinstance(moose.element(src),ReacBase) and (isinstance(moose.element(des),PoolBase) ) ):
- # moose.connect(src, 'prd', des, 'reac', 'OneToOne')
- # elif( isinstance(moose.element(src),EnzBase) and (isinstance(moose.element(des),PoolBase) ) ):
- # moose.connect(src, 'prd', des, 'reac', 'OneToOne')
elif( isinstance(moose.element(src),StimulusTable) and (isinstance(moose.element(des),PoolBase) ) ):
moose.connect(src, 'output', des, 'setConcInit', 'OneToOne')
else:
diff --git a/plugins/modelBuild.py b/plugins/modelBuild.py
index 406e0d2a4360a08c0489f25c2f9a782839a3bb2d..25579bfd3d113a03b0dbf29b348d4f800f4079d9 100644
--- a/plugins/modelBuild.py
+++ b/plugins/modelBuild.py
@@ -1,3 +1,12 @@
+__author__ = "HarshaRani"
+__credits__ = ["Upi Lab"]
+__license__ = "GPL3"
+__version__ = "1.0.0"
+__maintainer__ = "HarshaRani"
+__email__ = "hrani@ncbs.res.in"
+__status__ = "Development"
+__updated__ = "Jul 27 2017"
+
import moose
from kkitQGraphics import *
from kkitOrdinateUtil import *
@@ -25,7 +34,6 @@ 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
itemAtView = view.sceneContainerPt.itemAt(view.mapToScene(event_pos))