diff --git a/.travis.yml b/.travis.yml
index e5a702f37df471de18bff7d57ab95c8aebdbe434..15779bf198d587255777bc0c0afe4c636ee06f89 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,8 +7,6 @@ notifications:
install:
- - sudo apt-get clean
- - sudo apt-get update
- wget http://download.opensuse.org/repositories/home:moose/xUbuntu_12.04/Release.key
- sudo apt-key add - < Release.key
- sudo sh -c "echo 'deb http://download.opensuse.org/repositories/home:/moose/xUbuntu_12.04/ /' >> /etc/apt/sources.list.d/moose.list"
diff --git a/PlotWidgetContainer.py b/PlotWidgetContainer.py
index a9656203e3749a0f00b2917bb5555e4a46b5569f..f42e0a87e27ba9fe891b53344957d2f43a29b402 100644
--- a/PlotWidgetContainer.py
+++ b/PlotWidgetContainer.py
@@ -9,10 +9,10 @@ __author__ = "Aviral Goel"
__credits__ = ["Upi Lab"]
__license__ = "GPL3"
__version__ = "1.0.0"
-__maintainer__ = "Aviral Goel,HarshaRani"
+__maintainer__ = "Aviral Goel"
__email__ = "goel.aviral@gmail.com"
__status__ = "Development"
-__updated__ = "Feb 14 2017"
+
import sys
import os
@@ -49,8 +49,6 @@ 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:
@@ -89,18 +87,6 @@ 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 ac591c81dfcebf2fd6c940d05a629077fe870d43..458f7b389e3f566a83ce0e2fc6c98cfaa3e1ac74 100644
--- a/defaults.py
+++ b/defaults.py
@@ -13,9 +13,6 @@ FIELD_UNITS={
'Kd' : '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 b8574648e0528102c727f09fd66e940885cf813e..9f201303e2db36f325e27661637b37fbcfb7504a 100644
--- a/mgui.py
+++ b/mgui.py
@@ -6,9 +6,9 @@
# Maintainer:
# Created: Mon Nov 12 09:38:09 2012 (+0530)
# Version:
-# Last-Updated: Sat Mar 7 13:47:33 2017 (+0530)
+# Last-Updated: Fri Oct 30 11:54:33 2015 (+0530)
# By: Harsha
-# Update #:
+# Update #: 1338
# URL:
# Keywords:
# Compatibility:
@@ -206,7 +206,7 @@ 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" ),
- ("ReducedModel (200s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py"),
+ ("Reduced6 (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 +246,7 @@ 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] == "ReducedModel (200s)":
+ elif k[0] == "Reduced6 (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 +258,7 @@ class MWindow(QtGui.QMainWindow):
layout4.addWidget(button)
elif k[0] in ["Fig5A (20s)","Fig5BCD (240s)"]:
layout5.addWidget(button)
- elif k[0] in ["Fig6A (60s)","ReducedModel (200s)"]:
+ elif k[0] in ["Fig6A (60s)","Reduced6 (200s)"]:
layout6.addWidget(button)
elif k[0] in ["Squid"]:
layout7.addWidget(button)
@@ -476,12 +476,11 @@ class MWindow(QtGui.QMainWindow):
if name == 'kkit':
self.objectEditDockWidget.objectNameChanged.connect(self.plugin.getEditorView().getCentralWidget().updateItemSlot)
self.objectEditDockWidget.colorChanged.connect(self.plugin.getEditorView().getCentralWidget().updateColorSlot)
- #self.plugin.objectSolverChanged.connect(self.plugin.mainWindow.objectEditClearSlot)
self.setCurrentView('editor')
freeCursor()
return self.plugin
-
+
def updateExistingMenu(self, menu):
"""Check if a menu with same title
already exists. If so, update the same and return
@@ -565,7 +564,7 @@ class MWindow(QtGui.QMainWindow):
break
if newSubWindow:
subwin = self.mdiArea.addSubWindow(widget)
- title = widget.modelRoot
+ title = widget.modelRoot+'/model'
#subwin.setWindowTitle('%s: %s' % (view, widget.modelRoot))
subwin.setWindowTitle('%s: %s' % (view, title))
subwin.setSizePolicy(QtGui.QSizePolicy.Minimum |
@@ -642,67 +641,24 @@ 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" ),
- ("ReducedModel (200s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py"),
+ ("Reduced6 (200s)", "../moose-examples/paper-2015/Fig6_NetMultiscale/ReducedModel.py"),
("Squid" , "../moose-examples/squid/squid_demo.py")
])
-
- self.subMenu = QtGui.QMenu('Demos')
+ self.subMenu = QtGui.QMenu('Paper_2015_Demos')
for i in range(0,len(self.menuitems)):
k = self.menuitems.popitem(0)
- 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)
+ 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"))
elif k[0] == "Fig3B_Gssa (2s)":
- 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)
+ t.connect(t,QtCore.SIGNAL('triggered()'),lambda script = k[1]: self.run_genesis_script(script,"gssa"))
else:
- 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)
-
+ t.connect(t,QtCore.SIGNAL('triggered()'),lambda : self.run_python_script(k[1]))
+ self.subMenu.addAction(t)
self.fileMenu.addMenu(self.subMenu)
+
if not hasattr(self,'loadedModels'):
self.loadedModelAction = QtGui.QAction('Recently Loaded Models',self)
self.loadedModelAction.setCheckable(False)
@@ -1069,16 +1025,11 @@ class MWindow(QtGui.QMainWindow):
'''
#Harsha: added visible=True so that loadModelDialogSlot and NewModelDialogSlot call this function
# to clear out object path
-
def objectEditSlot(self, mobj, visible=True):
"""Slot for switching the current object in object editor."""
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
@@ -1154,27 +1105,20 @@ class MWindow(QtGui.QMainWindow):
ret = []
ret,pluginName = self.checkPlugin(dialog)
if pluginName == 'kkit':
- 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()
+ 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()
return
else:
- 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()
- return
- else:
- valid = True
+ valid = True
if valid == True:
modelAnno = moose.Annotator(ret['model'].path+'/info')
if ret['subtype']:
@@ -1214,7 +1158,6 @@ class MWindow(QtGui.QMainWindow):
#ret = loadFile(str(fileName), '/model/%s' % (modelName), merge=False)
#This will clear out object editor's objectpath and make it invisible
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'])
@@ -1222,8 +1165,7 @@ class MWindow(QtGui.QMainWindow):
pluginName = subtype_plugin_map['%s/%s' % (ret['modeltype'], ret['subtype'])]
except KeyError:
pluginName = 'default'
- if ret['foundlib']:
- print ('Loaded model %s' %(ret['model'].path))
+ print 'Loaded model', ret['model'].path
return ret,pluginName
def dialog_check(self,ret):
diff --git a/mload.py b/mload.py
index 8ee50546ee9c7ebcc1ed554b4d1a8ca8d3ab984e..257daa9410909a3fb8eb877afdf8ef7ff7d125b5 100644
--- a/mload.py
+++ b/mload.py
@@ -119,8 +119,6 @@ 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
"""
num = 1
- libsfound = True
- model = '/'
newTarget = target
while moose.exists(newTarget):
newTarget = target + "-" + str(num)
@@ -231,8 +229,7 @@ def loadFile(filename, target, solver="gsl", merge=True):
# app.restoreOverrideCursor()
return {'modeltype': modeltype,
'subtype': subtype,
- 'model': model,
- 'foundlib' :libsfound}
+ 'model': model}
#
diff --git a/objectedit.py b/objectedit.py
index b76257efd3800afe0eb3e85cb25569e7fcccaec8..a98294cc3f3fa619651e8ccf70f011bba1122810 100644
--- a/objectedit.py
+++ b/objectedit.py
@@ -193,7 +193,7 @@ 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):
@@ -236,18 +236,8 @@ class ObjectEditModel(QtCore.QAbstractTableModel):
else:
oldValue = self.mooseObject.getField(field)
- 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)
-
+ value = type(oldValue)(value)
+ tt = self.mooseObject.setField(field, value)
self.undoStack.append((index, oldValue))
if field == 'name':
self.emit(QtCore.SIGNAL('objectNameChanged(PyQt_PyObject)'), self.mooseObject)
@@ -257,7 +247,7 @@ 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()
@@ -427,7 +417,7 @@ class ObjectEditView(QtGui.QTableView):
self.setColor(getColor(self.model().mooseObject.path+'/info')[1])
except:
pass
- print ('Created view with %s' %(mobject))
+ print 'Created view with', mobject
def setColor(self, color):
self.colorButton.setStyleSheet(
@@ -472,8 +462,6 @@ class ObjectEditDockWidget(QtGui.QDockWidget):
# 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/kkit.py b/plugins/kkit.py
index 9c8f96ec5eb70f44c76b1e95c147f936d14fe591..68bfd85ee77dcfb1a38c00ffea00e794363bc74a 100644
--- a/plugins/kkit.py
+++ b/plugins/kkit.py
@@ -34,7 +34,6 @@ from setsolver import *
class KkitPlugin(MoosePlugin):
"""Default plugin for MOOSE GUI"""
- #objectSolverChanged = pyqtSignal()
def __init__(self, *args):
#print args
MoosePlugin.__init__(self, *args)
@@ -90,7 +89,7 @@ class KkitPlugin(MoosePlugin):
writeerror,consistencyMessages,writtentofile = moose.SBML.mooseWriteSBML(self.modelRoot,str(filename),self.coOrdinates)
if writeerror == -2:
#QtGui.QMessageBox.warning(None,'Could not save the Model','\n WriteSBML : This copy of MOOSE has not been compiled with SBML writing support.')
- QtGui.QMessageBox.warning(None,'python-libsbml is not found',consistencyMessages)
+ QtGui.QMessageBox.warning(None,'Could not save the Model',consistencyMessages)
elif writeerror == -1:
QtGui.QMessageBox.warning(None,'Could not save the Model','\n This model is not valid SBML Model, failed in the consistency check')
elif writeerror == 1:
@@ -233,7 +232,6 @@ class AnotherKkitRunView(RunView):
reinit = addSolver(modelRoot,solver)
if reinit:
self.getSchedulingDockWidget().widget().resetSimulation()
- #self.plugin.objectSolverChanged.emit()
#self.kkitRunView.getCentralWidget().addSolver(solver)
@@ -519,15 +517,12 @@ class KineticsWidget(EditorWidgetBase):
for funcObj in find_index(memb,'function'):
funcinfo = moose.element(funcObj).path+'/info'
- poolt = ["ZombieBufPool","BufPool","ZombiePool","Pool"]
- if funcObj.parent.className in poolt:
+ if funcObj.parent.className == "ZombieBufPool" or funcObj.parent.className == "BufPool":
funcinfo = moose.element(funcObj).path+'/info'
Af = Annotator(funcinfo)
funcParent =self.mooseId_GObj[element(funcObj.parent)]
-
elif funcObj.parent.className == "CubeMesh" or funcObj.parent.className == "CylMesh":
funcParent = self.qGraCompt[cmpt]
-
funcItem = FuncItem(funcObj,funcParent)
self.mooseId_GObj[element(funcObj.getId())] = funcItem
self.setupDisplay(funcinfo,funcItem,"Function")
@@ -571,14 +566,12 @@ class KineticsWidget(EditorWidgetBase):
if bgcolor.name() == "#ffffff" or bgcolor == "white":
bgcolor = getRandColor()
Annoinfo.color = str(bgcolor.name())
-
if isinstance(self,kineticEditorWidget):
funct = ["Function","ZombieFunction"]
comptt = ["CubeMesh","CylMesh"]
if objClass in funct:
- poolt = ["ZombieBufPool","BufPool","ZombiePool","Pool"]
-
+ poolt = ["ZombieBufPool","BufPool"]
if graphicalObj.mobj.parent.className in poolt:
xpos = 0
ypos = 30
@@ -586,7 +579,7 @@ class KineticsWidget(EditorWidgetBase):
xpos,ypos = self.positioninfo(info)
else:
xpos,ypos = self.positioninfo(info)
-
+
self.xylist = [xpos,ypos]
self.xyCord[moose.element(info).parent] = [xpos,ypos]
@@ -595,7 +588,6 @@ class KineticsWidget(EditorWidgetBase):
editorItem = self.editormooseId_GObj[moose.element(info).parent]
xpos = editorItem.scenePos().x()
ypos = editorItem.scenePos().y()
-
#Annoinfo.x = xpos
#Annoinfo.y = -ypos
graphicalObj.setDisplayProperties(xpos,ypos,textcolor,bgcolor)
@@ -621,13 +613,13 @@ 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])]
@@ -635,9 +627,9 @@ 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 ):
@@ -648,7 +640,7 @@ 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)
@@ -661,7 +653,7 @@ 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]
@@ -996,7 +988,7 @@ if __name__ == "__main__":
try:
filepath = '../../Demos/Genesis_files/'+modelPath+'.g'
filepath = '/home/harsha/genesis_files/gfile/'+modelPath+'.g'
- print( "%s" %(filepath))
+ print filepath
f = open(filepath, "r")
loadModel(filepath,'/'+modelPath)
@@ -1012,6 +1004,6 @@ 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 3b46a2c80502383b12429f3185eb1aef0d053212..e11ebe3ff29d3110751239f00782dd1f260143ed 100644
--- a/plugins/kkitCalcArrow.py
+++ b/plugins/kkitCalcArrow.py
@@ -1,6 +1,6 @@
from PyQt4.QtGui import QPolygonF
from PyQt4.QtCore import QLineF,QPointF
-from math import sin,cos,atan2,radians
+import math
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 +46,9 @@ def calcArrow(srcdes_list,itemignoreZooming,iconScale):
dy = desRect.center().y()- srcRect.center().y()
dx0 = dy
dy0 = -dx
- tetha1 = (atan2(dy0,dx0))
- a0 = 4 *(cos(tetha1))
- b0 = 4 *(sin(tetha1))
+ tetha1 = (math.atan2(dy0,dx0))
+ a0 = 4 *(math.cos(tetha1))
+ b0 = 4 *(math.sin(tetha1))
''' Higher order ( > 4) connectivity will not be done'''
if ((order == 3) or (order == 4)):
a0 = a0*2
@@ -154,9 +154,9 @@ def calcLineRectIntersection(rect, centerLine):
def arrowHead(srcAngle,degree,lineSpoint,iconScale):
''' arrow head is calculated '''
r = 8*iconScale
- delta = radians(srcAngle) + radians(degree)
- width = sin(delta)*r
- height = cos(delta)*r
+ delta = math.radians(srcAngle) + math.radians(degree)
+ width = math.sin(delta)*r
+ height = math.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 cb2c1f866d0873a04eba4c9293541915d5de40c1..cdd23bc7d1af6539e7bd077620f78488e023eed3 100644
--- a/plugins/kkitOrdinateUtil.py
+++ b/plugins/kkitOrdinateUtil.py
@@ -1,19 +1,5 @@
-__author__ = "HarshaRani"
-__credits__ = ["Upi Lab"]
-__license__ = "GPL3"
-__version__ = "1.0.0"
-__maintainer__ = "HarshaRani"
-__email__ = "hrani@ncbs.res.in"
-__status__ = "Development"
-__updated__ = "Feb 14 2017"
-
from moose import *
import numpy as np
-from moose import wildcardFind,element,PoolBase,CplxEnzBase,Annotator,exists
-import numpy as np
-import networkx as nx
-from networkx.drawing.nx_agraph import graphviz_layout
-
def setupMeshObj(modelRoot):
''' Setup compartment and its members pool,reaction,enz cplx under self.meshEntry dictionaries \
@@ -173,8 +159,6 @@ def autoCoordinates(meshEntry,srcdesConnection):
print " kkit Ordinatesutil autoCoordinates "
G = nx.Graph()
- #G = pgv.AGraph()
- positionInfo = {}
for cmpt,memb in meshEntry.items():
for enzObj in find_index(memb,'enzyme'):
#G.add_node(enzObj.path)
diff --git a/plugins/kkitQGraphics.py b/plugins/kkitQGraphics.py
index bbab5983ffa407da094ecfb3052061138c500883..b0bb4338871e106d8cee4094dc8c187d1ac22454 100644
--- a/plugins/kkitQGraphics.py
+++ b/plugins/kkitQGraphics.py
@@ -1,13 +1,3 @@
-
-__author__ = "HarshaRani"
-__credits__ = ["Upi Lab"]
-__license__ = "GPL3"
-__version__ = "1.0.0"
-__maintainer__ = "HarshaRani"
-__email__ = "hrani@ncbs.res.in"
-__status__ = "Development"
-__updated__ = "Mar 7 2017"
-
#import sys
#sys.path.insert(0, '/home/harsha/trunk/gui')
import config
@@ -15,7 +5,6 @@ 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"""
@@ -71,9 +60,7 @@ 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.funcImage = QImage('icons/classIcon/Function.png').scaled(15,33)
self.bg = QtGui.QGraphicsRectItem(self)
self.bg.setAcceptHoverEvents(True)
self.gobj = QtGui.QGraphicsPixmapItem(QtGui.QPixmap.fromImage(self.funcImage),self.bg)
@@ -87,12 +74,11 @@ class FuncItem(KineticsDisplayItem):
def setDisplayProperties(self,x,y,textcolor,bgcolor):
"""Set the display properties of this item."""
- #With Respect to BufPool (as parent which is in old genesis) then function are placed at 0,30 (which is below the BufPool)
+ #With Respect to BuffPool (as parent which is in old genesis) then function are placed at 0,30 (which is below the BuffPool)
#else if droped from the GUI then placed wrt position
#self.setGeometry(0, 30,self.gobj.boundingRect().width(),self.gobj.boundingRect().height())
#self.setGeometry(x,y)
- poolt = ["ZombieBufPool","BufPool","ZombiePool","Pool"]
- if self.gobj.mobj.parent.className in poolt:
+ if self.gobj.mobj.parent.className == "ZombieBufPool" or self.gobj.mobj.parent.className == "BufPool":
self.setGeometry(0, 30,self.gobj.boundingRect().width(),self.gobj.boundingRect().height())
else:
self.setGeometry(x,y,self.gobj.boundingRect().width(),self.gobj.boundingRect().height())
@@ -197,9 +183,6 @@ 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)))
@@ -495,9 +478,7 @@ class ComptItem(QtGui.QGraphicsRectItem):
self.setFlag(QtGui.QGraphicsItem.ItemIsMovable, True);
self.setFlag(QtGui.QGraphicsItem.ItemIsSelectable)
- #self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges, 1)
- QT_VERSION = str(QtCore.QT_VERSION_STR).split('.')
- QT_MINOR_VERSION = int(QT_VERSION[1])
+ #self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges, 1)
if config.QT_MINOR_VERSION >= 6:
self.setFlag(QtGui.QGraphicsItem.ItemSendsGeometryChanges, 1)
'''
diff --git a/plugins/modelBuild.py b/plugins/modelBuild.py
index 2fc00342e2fae32e98ebfa991529e7e6eb471ed3..406e0d2a4360a08c0489f25c2f9a782839a3bb2d 100644
--- a/plugins/modelBuild.py
+++ b/plugins/modelBuild.py
@@ -25,7 +25,7 @@ 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
+ print "28 ",modelpath
if moose.exists(modelpath+'/info'):
mType = moose.Annotator((moose.element(modelpath+'/info'))).modeltype
itemAtView = view.sceneContainerPt.itemAt(view.mapToScene(event_pos))
@@ -318,4 +318,4 @@ def findCompartment(mooseObj):
elif isinstance(mooseObj,ChemCompt):
return (mooseObj)
else:
- return findCompartment(moose.element(mooseObj.parent))
\ No newline at end of file
+ return findCompartment(moose.element(mooseObj.parent))