This file is indexed.

/usr/share/pyshared/Epigrass/neteditor.py is in epigrass 2.0.4-3.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

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# -*- coding: utf-8 -*-

"""
Module implementing MainWindow.
"""
from PyQt4 import QtCore, QtGui
from PyQt4.QtGui import QMainWindow
from PyQt4.QtCore import pyqtSignature

from Ui_neteditor import Ui_MainWindow
from data_io import  loadData
import networkx as nx
#import dgraph
import math
from numpy import array
import elasticnodes as dgraph

class MainWindow(QMainWindow, Ui_MainWindow):
    """
    Class documentation goes here.
    """
    def __init__(self, parent = None):
        """
        Constructor
        """
        QMainWindow.__init__(self, parent)
        self.setupUi(self)
        self.network = None
        self.Map = None
        self.filename = None
    
    @pyqtSignature("QPoint")
    def on_centralWidget_customContextMenuRequested(self, pos):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        raise NotImplementedError
    
    @pyqtSignature("QPoint")
    def on_graphicsView_customContextMenuRequested(self, pos):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        raise NotImplementedError
    
    @pyqtSignature("QPoint")
    def on_edgeTable_customContextMenuRequested(self, pos):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        pass
    
    @pyqtSignature("")
    def on_edgeTable_itemSelectionChanged(self):
        """
        Slot documentation goes here.
        """
        pass
    
    @pyqtSignature("int, int")
    def on_edgeTable_cellDoubleClicked(self, row, column):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        pass
    
    @pyqtSignature("int, int")
    def on_edgeTable_cellActivated(self, row, column):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        pass
    
    @pyqtSignature("QPoint")
    def on_nodeTable_customContextMenuRequested(self, pos):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        raise NotImplementedError
    
    @pyqtSignature("QTableWidgetItem*")
    def on_nodeTable_itemActivated(self, item):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        raise NotImplementedError
    
    @pyqtSignature("")
    def on_nodeTable_itemSelectionChanged(self):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        raise NotImplementedError
    
    @pyqtSignature("int, int")
    def on_nodeTable_cellActivated(self, row, column):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        raise NotImplementedError
    
    @pyqtSignature("QAction*")
    def on_toolBar_actionTriggered(self, action):
        """
        Slot documentation goes here.
        """
        pass
    
    @pyqtSignature("")
    def on_actionOpen_edges_file_activated(self):
        """
        Slot documentation goes here.
        """
        fname = str(QtGui.QFileDialog.getOpenFileName(\
            None,
            self.trUtf8("Select an Epigrass edges file"),
            self.trUtf8("."),
            self.trUtf8("*.csv;;*.*"),
            None))
        self.filename = fname
        self.network = Network(self.graphicsView)
        edgelist = loadData(fname, ',')
        nodelist  = set([])
        header = edgelist.pop(0)
        
        self.edgeTable.setColumnCount(len(header))
        self.edgeTable.setRowCount(len(edgelist))
        self.edgeTable.setHorizontalHeaderLabels(header)
        print self.edgeTable.rowCount()
        for i,e in enumerate(edgelist):
            nodelist.add(e[5])
            nodelist.add(e[6])
            self.network.G.add_edge(e[5], e[6], {'weight':e[2], 'source_name':e[0], 'dest_name':e[1]}) #edge weight is flow S->D
            for j,v in enumerate(e):
                item  = QtGui.QTableWidgetItem(v)
                self.edgeTable.setItem(i,j,item)
        print self.edgeTable.takeItem(0,0).text()
        # Fill nodes table
        self.nodeTable.setColumnCount(1)
        self.nodeTable.setRowCount(len(nodelist))
        self.nodeTable.setHorizontalHeaderLabels(['Geocode'])
        for i,n in enumerate(nodelist):
            item = QtGui.QTableWidgetItem(n)
            self.nodeTable.setItem(i,0,item)
                
    
    @pyqtSignature("")
    def on_actionOpen_Shapefile_activated(self):
        """
        Slot documentation goes here.
        """
        fname = str(QtGui.QFileDialog.getOpenFileName(\
            None,
            self.trUtf8("Select a Shapefile"),
            self.trUtf8("."),
            self.trUtf8("*.shp"),
            None))
    
    @pyqtSignature("")
    def on_action_Save_activated(self):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        raise NotImplementedError
    
    @pyqtSignature("")
    def on_actionSave_as_activated(self):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        raise NotImplementedError
    
    @pyqtSignature("")
    def on_action_Graph_activated(self):
        """
        Slot documentation goes here.
        """
        if  self.network:
            nlist = []
            for k, v in self.network.getLayout().iteritems():
                nlist.append((k, v[0]*100, v[1]*100, str(k)))
            self.network.drawGraph(nlist, self.network.G.edges())
            
    
    @pyqtSignature("")
    def on_actionE_xit_activated(self):
        """
        Closes the network editor main window
        """
        self.close()
    
    @pyqtSignature("")
    def on_actionStats_activated(self):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        raise NotImplementedError
    
    @pyqtSignature("")
    def on_actionCheck_Graph_activated(self):
        """
        Slot documentation goes here.
        """
        # TODO: not implemented yet
        raise NotImplementedError
    
    @pyqtSignature("")
    def on_actionDot_activated(self):
        """
        Slot documentation goes here.
        """
        if self.network:
            nx.write_dot(self.network.G, self.filename.split('.')[0]+'.dot')
    
    @pyqtSignature("")
    def on_actionGML_activated(self):
        """
        Slot documentation goes here.
        """
        if self.network:
            nx.write_gml(self.network.G, self.filename.split('.')[0]+'.gml')
    
    @pyqtSignature("")
    def on_actionPajek_activated(self):
        """
        Slot documentation goes here.
        """
        if self.network:
            nx.write_pajek(self.network.G, self.filename.split('.')[0]+'.pajek')
    
    @pyqtSignature("")
    def on_actionYAML_activated(self):
        """
        Slot documentation goes here.
        """
        if self.network:
            nx.write_yaml(self.network.G, self.filename.split('.')[0]+'.yaml')

class Network:
    '''
    This class handle every network related
    methods, from analysis  to drawing.
    '''
    def __init__(self, displaywidget):
        self.View = displaywidget
        self.View.scene = QtGui.QGraphicsScene(self.View)
        self.N = Graph()
        self.G = nx.DiGraph(multiedges=True)

    def getLayout(self):
        return nx.random_layout(self.G)
        
    def drawGraph(self, nlist, elist):
        '''
        Draws Graph object representing the network
        '''
        npos= [(n[1], -n[2]) for n in nlist]
        xmin,ymin = array(npos).min(axis=0)
        xmax,ymax = array(npos).max(axis=0)
        for n in nlist:
            node = Node(self.N, n[0], n[3])
            node.setPos(*(n[1], -n[2]))
            node.size = max(xmax-xmin, ymax-ymin)/math.sqrt(len(nlist))*0.5
            self.View.scene.addItem(node)
            self.N.insertNode(node)
            #print node.x(), node.y(), n.center[0], n.center[1]
        self.View.nodes = self.N.nodes
       
        asz = max(xmax-xmin, ymax-ymin)/math.sqrt(len(nlist))*0.2 #arrow size
        for e in elist:
            ed = Edge(self.N.polyDict[e[0]], self.N.polyDict[e[1]])
            ed.arrowSize = asz
            self.View.scene.addItem(ed)
            self.N.insertEdge(ed)
        self.xmax, self.xmin = xmax, xmin
        self.ymax, self.ymin = ymax, ymin
        self.centerScene()
        
    def centerScene(self):
        """
        centers the scene and fits the specified rectangle to it
        """
        ymax, ymin = self.ymax, self.ymin
        xmax, xmin = self.xmax, self.xmin
        xxs = (xmax-xmin)*1.1 #percentage of extra space
        yxs = (ymax-ymin)*1.1 #percentage of extra space
        #calculating center of scene

        xc = (xmax+xmin)/2. 
        yc = (ymax+ymin)/2.
        self.View.scene.setItemIndexMethod(QtGui.QGraphicsScene.NoIndex)
        self.View.scene.setSceneRect(xmin, ymin, xxs, yxs)
#        print self.mapView.scene.width(), self.mapView.scene.height()
        self.View.fitInView(xmin, ymin, xxs, yxs)
        self.View.setScene(self.View.scene)
        self.View.updateSceneRect(self.View.scene.sceneRect())
        self.View.centerOn(xc, yc)
        scale_factor = self.View.width()/xxs
        self.View.scale(scale_factor, scale_factor)
        
        self.View.setCacheMode(QtGui.QGraphicsView.CacheBackground)
        self.View.setRenderHint(QtGui.QPainter.Antialiasing)
        self.View.setTransformationAnchor(QtGui.QGraphicsView.AnchorUnderMouse)
        self.View.setResizeAnchor(QtGui.QGraphicsView.AnchorViewCenter)
        
class Graph(object):
    """
    The Graph.self.data(start)[5]
    """
    def __init__(self, **keywords):
        """
        Construct a Graph.
        """
        self.map = None
        self.nodes = []
        self.edges = []
        self.dragObject = None
        self.click = None
        self.distance = None
        self.timelabel = None
        self.rememberFixed = None
        self.rememberColor = None
#        self.display = display
        self.polyDict = {}#dictionary of nodes by geocode
        self.rect = [0,0,0,0]#xmin,ymin,xmax,ymax

    def insertNode(self, node):
        """
        Insert node into the system.
\        """
        #needs to be a list because the node index in this list identify it within the graph.

        #FIXME: verify time overhead of this check
        if not node in self.nodes:
            self.nodes.append(node)
            self.polyDict[node.geocode] = node
            node.graph = self #pass a reference of self to the node.

    def insertMap(self,map_):
        """
        Insert map into the system.
        """
        self.map = map_
        map_.graph = self

    def insertNodeList(self, nodelist):
        """
        Insert all Nodes in nodelist into the system.
        """

        map(self.insertNode, nodelist)

    def insertEdge(self, edge):
        """
        Insert edge into the system.
        """
        if edge not in self.edges:
            self.edges.append(edge)

    def insertEdgeList(self, edgelist):
        """
        Insert all Edges in edgelist into the system.
        """
        map(self.insertEdge, edgelist)

    def getEdgeFromMatrix(self, matrix):
        """
        Extract edges from the adjacency matrix.
        """
        #FIXME: eitehr integrate this into the graph object, or make it a separate function
        siz = matrix.shape[0]
        el = []
        for c in xrange(siz):
            for l in xrange(c+1): #scans only the lower triangle
                if matrix[l,c]:
                    el.append((c,l))
        return el


    def centerView(self):
        pass

    def getRect(self):
        '''
        Returns the bounding rectangle for the graph
        '''
        for n in self.nodes:
            self.rect[0] = n.pos.x() if n.pos.x()<self.rect[0] else self.rect[0]
            self.rect[1] = n.pos.y() if n.pos.y()<self.rect[1] else self.rect[1]
            self.rect[2] = n.pos.x() if n.pos.x()>self.rect[2] else self.rect[2]
            self.rect[3] = n.pos.y() if n.pos.y()>self.rect[3] else self.rect[3]
        return self.rect


class Node(QtGui.QGraphicsItem):
    Type = QtGui.QGraphicsItem.UserType + 1

    def __init__(self, graphWidget, geocode, name):
        QtGui.QGraphicsItem.__init__(self)

        self.graph = graphWidget
        self.edgeList = []
        self.newPos = QtCore.QPointF()
#        self.setFlag(QtGui.QGraphicsItem.ItemIsMovable)
        self.setZValue(1)
        self.geocode = geocode
        self.name = name
        self.size  = 20
        

    def type(self):
        return Node.Type

    def addEdge(self, edge):
        self.edgeList.append(edge)
        edge.adjust()

    def edges(self):
        return self.edgeList


    def boundingRect(self):
        adjust = 2.0
        return QtCore.QRectF(-10 - adjust, -10 - adjust,
                             23 + adjust, 23 + adjust)

    def shape(self):
        path = QtGui.QPainterPath()
        path.addEllipse(-self.size/2., -self.size/2., self.size,self.size)
        return path

    def paint(self, painter, option, widget):
#        painter.setPen(QtCore.Qt.NoPen)
#        painter.setBrush(QtCore.Qt.darkGray)
#        painter.drawEllipse(-self.size/2.*.8, -self.size/2.*.8, self.size,self.size)

        gradient = QtGui.QRadialGradient(-3, -3, 10)
        if option.state & QtGui.QStyle.State_Sunken:
            gradient.setCenter(3, 3)
            gradient.setFocalPoint(3, 3)
            gradient.setColorAt(1, QtGui.QColor(QtCore.Qt.yellow).light(120))
            gradient.setColorAt(0, QtGui.QColor(QtCore.Qt.darkYellow).light(120))
        else:
            gradient.setColorAt(0, QtCore.Qt.yellow)
            gradient.setColorAt(1, QtCore.Qt.darkYellow)

        painter.setBrush(QtGui.QBrush(gradient))
        painter.setPen(QtGui.QPen(QtCore.Qt.black, 0))
        painter.drawEllipse(-self.size/2., -self.size/2., self.size,self.size)

#        return QtGui.QGraphicsItem.itemChange(self, change, value)

    def mousePressEvent(self, event):
        self.update()
        QtGui.QGraphicsItem.mousePressEvent(self, event)

    def mouseReleaseEvent(self, event):
        self.update()
        QtGui.QGraphicsItem.mouseReleaseEvent(self, event)

class Edge(QtGui.QGraphicsItem):
    Pi = math.pi
    TwoPi = 2.0 * Pi

    Type = QtGui.QGraphicsItem.UserType + 2

    def __init__(self, sourceNode, destNode):
        QtGui.QGraphicsItem.__init__(self)
        self.arrowSize = 10.0
        self.sourcePoint = QtCore.QPointF()
        self.destPoint = QtCore.QPointF()
        self.setAcceptedMouseButtons(QtCore.Qt.NoButton)
        self.source = sourceNode
        self.dest = destNode
        self.source.addEdge(self)
        self.dest.addEdge(self)
        self.adjust()

    def type(self):
        return Edge.Type

    def sourceNode(self):
        return self.source

    def setSourceNode(self, node):
        self.source = node
        self.adjust()

    def destNode(self):
        return self.dest

    def setDestNode(self, node):
        self.dest = node
        self.adjust()

    def adjust(self):
        if not self.source or not self.dest:
            return

        line = QtCore.QLineF(self.mapFromItem(self.source, 0, 0), self.mapFromItem(self.dest, 0, 0))
        length = line.length()
        fac = self.source.size/2.5
        if length == 0.0:
            return

        edgeOffset = QtCore.QPointF((line.dx() * fac) / length, (line.dy() * fac) / length)

        self.prepareGeometryChange()
        self.sourcePoint = line.p1() + edgeOffset
        self.destPoint = line.p2() - edgeOffset

    def boundingRect(self):
        if not self.source or not self.dest:
            return QtCore.QRectF()

        penWidth = 1
        extra = (penWidth + self.arrowSize) / 2.0

        return QtCore.QRectF(self.sourcePoint,
                             QtCore.QSizeF(self.destPoint.x() - self.sourcePoint.x(),
                                           self.destPoint.y() - self.sourcePoint.y())).normalized().adjusted(-extra, -extra, extra, extra)

    def paint(self, painter, option, widget):
        if not self.source or not self.dest:
            return

        # Draw the line itself.
        line = QtCore.QLineF(self.sourcePoint, self.destPoint)

        if line.length() == 0.0:
            return

        painter.setPen(QtGui.QPen(QtCore.Qt.black, .1, QtCore.Qt.SolidLine, QtCore.Qt.RoundCap, QtCore.Qt.RoundJoin))
        painter.drawLine(line)

        # Draw the arrows if there's enough room.
        angle = math.acos(line.dx() / line.length())
        if line.dy() >= 0:
            angle = Edge.TwoPi - angle

        sourceArrowP1 = self.sourcePoint + QtCore.QPointF(math.sin(angle + Edge.Pi / 3) * self.arrowSize,
                                                          math.cos(angle + Edge.Pi / 3) * self.arrowSize)
        sourceArrowP2 = self.sourcePoint + QtCore.QPointF(math.sin(angle + Edge.Pi - Edge.Pi / 3) * self.arrowSize,
                                                          math.cos(angle + Edge.Pi - Edge.Pi / 3) * self.arrowSize);   
        destArrowP1 = self.destPoint + QtCore.QPointF(math.sin(angle - Edge.Pi / 3) * self.arrowSize,
                                                      math.cos(angle - Edge.Pi / 3) * self.arrowSize)
        destArrowP2 = self.destPoint + QtCore.QPointF(math.sin(angle - Edge.Pi + Edge.Pi / 3) * self.arrowSize,
                                                      math.cos(angle - Edge.Pi + Edge.Pi / 3) * self.arrowSize)

        painter.setBrush(QtCore.Qt.black)
        painter.drawPolygon(QtGui.QPolygonF([line.p1(), sourceArrowP1, sourceArrowP2]))
        painter.drawPolygon(QtGui.QPolygonF([line.p2(), destArrowP1, destArrowP2]))

if __name__ == "__main__":
    import sys
    app = QtGui.QApplication(sys.argv)
    MainW= QtGui.QMainWindow()
    ui = MainWindow()
    ui.show()
    sys.exit(app.exec_())