diff --git a/PlotWidgetContainer.py b/PlotWidgetContainer.py
index f42e0a87e27ba9fe891b53344957d2f43a29b402..a9656203e3749a0f00b2917bb5555e4a46b5569f 100644
--- a/PlotWidgetContainer.py
+++ b/PlotWidgetContainer.py
@@ -9,10 +9,10 @@ __author__ = "Aviral Goel"
__credits__ = ["Upi Lab"]
__license__ = "GPL3"
__version__ = "1.0.0"
-__maintainer__ = "Aviral Goel"
+__maintainer__ = "Aviral Goel,HarshaRani"
__email__ = "goel.aviral@gmail.com"
__status__ = "Development"
-
+__updated__ = "Feb 14 2017"
import sys
import os
@@ -49,6 +49,8 @@ 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 +89,18 @@ 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/mgui.py b/mgui.py
index ede1ba954889a588d8ef37f41645daa6d0f0ec13..30790dd3bd5b4183746c6627a1be35fba3bce4b1 100644
--- a/mgui.py
+++ b/mgui.py
@@ -6,7 +6,7 @@
# Maintainer:
# Created: Mon Nov 12 09:38:09 2012 (+0530)
# Version:
-# Last-Updated: Fri Oct 30 11:54:33 2015 (+0530)
+# Last-Updated: Tue Feb 14 15:20:33 2017 (+0530)
# By: Harsha
# Update #: 1338
# URL:
@@ -564,7 +564,7 @@ class MWindow(QtGui.QMainWindow):
break
if newSubWindow:
subwin = self.mdiArea.addSubWindow(widget)
- title = widget.modelRoot+'/model'
+ title = widget.modelRoot
#subwin.setWindowTitle('%s: %s' % (view, widget.modelRoot))
subwin.setWindowTitle('%s: %s' % (view, title))
subwin.setSizePolicy(QtGui.QSizePolicy.Minimum |
@@ -1105,20 +1105,27 @@ 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
+ compt = moose.wildcardFind(ret['model'].path+'/##[ISA=ChemCompt]')
+ if not len(compt):
+ reply = QtGui.QMessageBox.question(self, "Model is empty","Model has no compartment, atleast one compartment should exist to display the widget\n Do you want another file",
+ QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
+ if reply == QtGui.QMessageBox.Yes:
+ dialog = LoaderDialog(self,self.tr('Load model from file'))
+ if dialog.exec_():
+ ret,pluginName = self.checkPlugin(dialog)
+ ret,valid = self.dialog_check(ret)
+ else:
+ QtGui.QApplication.restoreOverrideCursor()
+ return
+ else:
+ valid = True
if valid == True:
modelAnno = moose.Annotator(ret['model'].path+'/info')
if ret['subtype']:
@@ -1148,7 +1155,8 @@ class MWindow(QtGui.QMainWindow):
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', ret['model'].path
return ret,pluginName
def dialog_check(self,ret):
diff --git a/mload.py b/mload.py
index b91e2888592a75138554a28521cb0f1fea98c218..cf0aeccd0c0cf2d4cfd74c254ba823085b1d5bb1 100644
--- a/mload.py
+++ b/mload.py
@@ -118,6 +118,8 @@ def loadFile(filename, target, solver="gsl", merge=True):
modelroot: root element of the model, None if could not be located - as is the case with Python scripts
"""
num = 1
+ libsfound = True
+ model = '/'
newTarget = target
while moose.exists(newTarget):
newTarget = target + "-" + str(num)
@@ -184,13 +186,21 @@ def loadFile(filename, target, solver="gsl", merge=True):
# moose.move("cells/", cell.path)
elif subtype == 'sbml':
- if target != '/':
- if moose.exists(target):
- moose.delete(target)
- model = mooseReadSBML(filename,target)
- if moose.exists(moose.element(model).path):
- moose.Annotator(moose.element(model).path+'/info').modeltype = "sbml"
- addSolver(target,'gsl')
+ foundLibSBML_ = False
+ try:
+ import libsbml
+ foundLibSBML_ = True
+ except ImportError:
+ pass
+ if foundLibSBML_:
+ if target != '/':
+ if moose.exists(target):
+ moose.delete(target)
+ model = mooseReadSBML(filename,target)
+ if moose.exists(moose.element(model).path):
+ moose.Annotator(moose.element(model).path+'/info').modeltype = "sbml"
+ addSolver(target,'gsl')
+ libsfound = foundLibSBML_
else:
raise FileLoadError('Do not know how to handle this filetype: %s' % (filename))
moose.setCwe(pwe) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour
@@ -200,7 +210,8 @@ def loadFile(filename, target, solver="gsl", merge=True):
# app.restoreOverrideCursor()
return {'modeltype': modeltype,
'subtype': subtype,
- 'model': model}
+ 'model': model,
+ 'foundlib' :libsfound}
diff --git a/plugins/kkit.py b/plugins/kkit.py
index 5b79ea6fa2514f7fa9968b412d210f904cfdf03f..8709044aeb1ddefc9b4917ebbdbc909c620459e8 100644
--- a/plugins/kkit.py
+++ b/plugins/kkit.py
@@ -1,3 +1,13 @@
+
+__author__ = "HarshaRani"
+__credits__ = ["Upi Lab"]
+__license__ = "GPL3"
+__version__ = "1.0.0"
+__maintainer__ = "HarshaRani"
+__email__ = "hrani@ncbs.res.in"
+__status__ = "Development"
+__updated__ = "Feb 14 2017"
+
import sys
from PyQt4 import QtGui, QtCore, Qt
from default import *
@@ -78,7 +88,7 @@ class KkitPlugin(MoosePlugin):
writeerror,consistencyMessages,writtentofile = moose.SBML.mooseWriteSBML(self.modelRoot,str(filename),self.coOrdinates)
if writeerror == -2:
#QtGui.QMessageBox.warning(None,'Could not save the Model','\n WriteSBML : This copy of MOOSE has not been compiled with SBML writing support.')
- QtGui.QMessageBox.warning(None,'Could not save the Model',consistencyMessages)
+ QtGui.QMessageBox.warning(None,'python-libsbml is not found',consistencyMessages)
elif writeerror == -1:
QtGui.QMessageBox.warning(None,'Could not save the Model','\n This model is not valid SBML Model, failed in the consistency check')
elif writeerror == 1:
@@ -592,7 +602,7 @@ class KineticsWidget(EditorWidgetBase):
comptt = ["CubeMesh","CylMesh"]
if objClass in funct:
- poolt = ["ZombieBufPool","BufPool"]
+ poolt = ["ZombieBufPool","BufPool","ZombiePool","Pool"]
if graphicalObj.mobj.parent.className in poolt:
xpos = 0
ypos = 30
diff --git a/plugins/kkitOrdinateUtil.py b/plugins/kkitOrdinateUtil.py
index a4ac1bc2cd425fc4d47b1bc8c40fd39f35fb52fe..dcfeb8ac9df78d8f39096ea9c97d800194ea4f99 100644
--- a/plugins/kkitOrdinateUtil.py
+++ b/plugins/kkitOrdinateUtil.py
@@ -1,8 +1,18 @@
+__author__ = "HarshaRani"
+__credits__ = ["Upi Lab"]
+__license__ = "GPL3"
+__version__ = "1.0.0"
+__maintainer__ = "HarshaRani"
+__email__ = "hrani@ncbs.res.in"
+__status__ = "Development"
+__updated__ = "Feb 14 2017"
+
from moose import *
import numpy as np
-import networkx as nx
from collections import Counter
-
+import networkx as nx
+from networkx.drawing.nx_agraph import graphviz_layout
+#import pygraphviz as pgv
def xyPosition(objInfo,xory):
try:
return(float(element(objInfo).getField(xory)))
@@ -181,6 +191,8 @@ def autoCoordinates(meshEntry,srcdesConnection):
ymin = 0.0
ymax = 1.0
G = nx.Graph()
+ #G = pgv.AGraph()
+ positionInfo = {}
for cmpt,memb in meshEntry.items():
for enzObj in find_index(memb,'enzyme'):
#G.add_node(enzObj.path)
@@ -218,17 +230,10 @@ def autoCoordinates(meshEntry,srcdesConnection):
else:
for items in (items for items in out ):
G.add_edge(element(items[0]).path,inn.path)
- position = nx.spring_layout(G)
- #nx.draw(G,pos=nx.spring_layout(G))
- #position = nx.spring_layout(G)
- #import matplotlib.pyplot as plt
- #plt.savefig('test.png')
- #position = nx.graphviz_layout(G, prog = 'dot')
- #agraph = nx.to_agraph(G)
- #agraph.draw("test.png", format = 'png', prog = 'dot')
xcord = []
ycord = []
+ position = graphviz_layout(G)
for item in position.items():
xy = item[1]
ann = moose.Annotator(item[0]+'/info')
@@ -237,6 +242,34 @@ def autoCoordinates(meshEntry,srcdesConnection):
ann.y = xy[1]
ycord.append(xy[1])
+ '''
+ if int( nx.__version__.split( '.' )[-1] ) >= 11:
+ position = nx.spring_layout( G )
+ else:
+ position = nx.graphviz_layout(G, prog = 'dot')
+ for item in position.items():
+ xy = item[1]
+ ann = moose.Annotator(item[0]+'/info')
+ ann.x = xy[0]
+ xcord.append(xy[0])
+ ann.y = xy[1]
+ ycord.append(xy[1])
+ '''
+ '''
+ #pygraphviz
+ G.layout()
+ for n in G.nodes():
+ print "inside 250 "
+ value = str(n.attr['pos'])
+ valuelist = (value.split(','))
+ positionInfo[(moose.element(n)).path] ={'x':float(valuelist[0]),'y':float(valuelist[1])}
+ ann = moose.Annotator(moose.element(n).path+'/info')
+ ann.x = float(valuelist[0])
+ ann.y = float(valuelist[1])
+
+ xcord.append(float(valuelist[0]))
+ xcord.append(float(valuelist[1]))
+ '''
if xcord and ycord:
xmin = min(xcord)
xmax = max(xcord)