From 0e72b3301760d6cccae4eaf34197c052bddddb20 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Tue, 31 Oct 2017 18:39:47 +0530
Subject: [PATCH] Squashed 'moose-gui/' changes from 38da92b04..5d7f7633f
5d7f7633f Too many python3 incompatibility issues. For now on, gui is only compatible with python2.
599dbd6d3 Testing with python3 as well. If python3 support is not intented, we can fallback this commit.
83be02e60 changes made after addition of groups, some of action are implemented
24cba7d6f some more clean
cdf16259d at file load dialog, a clean round trip is done
08fc6cd0b at loading time, kkit model is checked for the atleast for 1 compartment and atleast 2 species
373efaa6d check if moose object already exist, if yes use element, else create a object
e37368553 in mousePressEvent further check made for group object along with compartment and other moose object
ae6265ed8 travis is failing, while installing python-libsbml trying to fix providing -H
c70f30098 some clean up with co-ordinates while saving into XML files
dd177002c wrong comparsion with path and moose object was done corrected
24ecdccac some clean up with groups
84be91147 changes made related to group
5a6c654c7 Merge branch 'master' of https://github.com/BhallaLab/moose-gui
3fcc20a66 mgui in cleanup in dialog box, mload: sbml reader returns modelpath and errormsg, kkit: co-ordinates for sbml(auto co-ordinates) values are kept in annotation as its and while displayed as its, but for genesis default scenewidth and height is taken care and kkitOrdinatesUtil: sbml auto co-ordinates are kept as its
d93fd2118 hover overcompartment shows name and some more cleaned up after the bad merger 320e525a5a34fbd3f1cb572b6de38eca0c0876f0 and also wrong commit from 6fc726e
ed79c3980 indentation correction and missing lib
f4d880f53 Cleaned up, these 9 files after the bad merger 320e525a5a34fbd3f1cb572b6de38eca0c0876f0 and also wrong commit from 6fc726e560556f7619e31fe022ef094793d6a13a
2c594c457 in gui stoich.status along with warning, which Reac and Enz are dangling is also displayed in the QMessageBox
git-subtree-dir: moose-gui
git-subtree-split: 5d7f7633f5e20d48e4bfa0a2b38697c4d0d60d6a
---
.travis.yml | 2 +-
PlotWidgetContainer.py | 18 +-
defaults.py | 13 +-
mgui.py | 162 +++++++++---
mload.py | 87 ++++---
objectedit.py | 25 +-
plugins/constants.py | 24 +-
plugins/default.py | 47 +++-
plugins/kkit.py | 363 +++++++++++++++++---------
plugins/kkitCalcArrow.py | 23 +-
plugins/kkitOrdinateUtil.py | 311 ++++++++++++++++++++--
plugins/kkitQGraphics.py | 77 +++++-
plugins/kkitUtil.py | 50 +++-
plugins/kkitViewcontrol.py | 503 +++++++++++++++++-------------------
plugins/modelBuild.py | 10 +-
15 files changed, 1175 insertions(+), 540 deletions(-)
diff --git a/.travis.yml b/.travis.yml
index 15779bf1..b2967457 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 f42e0a87..d51ab81e 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 458f7b38..f7a51380 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 9f201303..24d2bf83 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 257daa94..9fc753e6 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 a98294cc..dcb019a4 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 558b5fc5..3596f2c5 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 ccf8846d..788e8349 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 68bfd85e..b6f7fb5a 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 e11ebe3f..4a3128f2 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 cdd23bc7..dd3b967d 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 b0bb4338..1f180190 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 a83a496c..71859880 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 c9541743..7d639504 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 406e0d2a..25579bfd 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))
--
GitLab