SelectPredictorsLayers.py

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## This file is part of the Software for Assisted Habitat Modeling package
## for VisTrails.
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from PyQt4 import QtCore, QtGui
import csv
import utils
from utils import writetolog
import shutil
import os
import subprocess

try:
    from vistrails.core.modules.vistrails_module import Module
    from vistrails.core.system import execute_cmdline
except:
    from core.modules.vistrails_module import Module
    from core.system import execute_cmdline
    
try:
    _fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
    _fromUtf8 = lambda s: s

class SelectListDialog(QtGui.QDialog):

    def __init__(self, kwargs, parent=None):
        #print inputMDS, outputMDS, rPath, modelsPath
        self.rPath = kwargs['r_path']
        self.kwargs = kwargs
        if not self.kwargs.has_key('numPlots'):
            self.kwargs['numPlots'] = 8
        if not self.kwargs.has_key('minCor'):
            self.kwargs['minCor'] = "0.7"
        
        self.selection_name = os.path.split(kwargs['outputMDS'])[1]
        self.selection_name = os.path.splitext(self.selection_name)[0]
        self.selection_name = self.selection_name.split('_')[-1]
        self.module = self.kwargs['module']
        self.displayJPEG = kwargs['displayJPEG']
        
        QtGui.QDialog.__init__(self, parent)
        
        self.inputMDS = kwargs['inputMDS']
        self.outputMDS = kwargs['outputMDS']
        self.outputDir = os.path.split(kwargs['outputMDS'])[0]
        
        layout = QtGui.QVBoxLayout()
        self.setWindowFlags(QtCore.Qt.Window)
        
        self.horizontalLayout_4 = QtGui.QHBoxLayout()
        self.horizontalLayout_4.setSpacing(5)
        self.horizontalLayout_4.setMargin(5)
        self.horizontalLayout_4.setObjectName(_fromUtf8("horizontalLayout_4"))
        self.verticalLayout_3 = QtGui.QVBoxLayout()
        self.verticalLayout_3.setObjectName(_fromUtf8("verticalLayout_3"))
        self.splitter = QtGui.QSplitter()
        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
        sizePolicy.setHorizontalStretch(0)
        sizePolicy.setVerticalStretch(0)
        sizePolicy.setHeightForWidth(self.splitter.sizePolicy().hasHeightForWidth())
        self.splitter.setSizePolicy(sizePolicy)
        self.splitter.setMinimumSize(QtCore.QSize(0, 0))
        self.splitter.setFrameShape(QtGui.QFrame.Box)
        self.splitter.setFrameShadow(QtGui.QFrame.Plain)
        self.splitter.setLineWidth(1)
        self.splitter.setOrientation(QtCore.Qt.Horizontal)
        self.splitter.setHandleWidth(10)
        self.splitter.setObjectName(_fromUtf8("splitter"))
        self.widget = QtGui.QWidget(self.splitter)
        self.widget.setObjectName(_fromUtf8("widget"))
        self.verticalLayout = QtGui.QVBoxLayout(self.widget)
        self.verticalLayout.setSpacing(4)
        self.verticalLayout.setSizeConstraint(QtGui.QLayout.SetDefaultConstraint)
        self.verticalLayout.setContentsMargins(6, 6, 3, 3)
        self.verticalLayout.setObjectName(_fromUtf8("verticalLayout"))
        self.label_2 = QtGui.QLabel(self.widget)
        self.label_2.setObjectName(_fromUtf8("label_2"))
        self.verticalLayout.addWidget(self.label_2)
        self.treeview = QtGui.QTreeWidget(self.widget)
        self.treeview.setColumnCount(2)
        self.treeview.setSortingEnabled(True)
        self.treeview.headerItem().setText(0, "Include")
        self.treeview.setColumnWidth(0,130)
        self.treeview.headerItem().setText(1, "% Deviance Explained")
        self.treeview.setColumnWidth(1, 125)
        self.treeview.setToolTip(_fromUtf8("Double click to view detailed information for single covariate."))
#        self.treeview.setHeaderLabels(['include', 'covariate'])
        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Ignored, QtGui.QSizePolicy.Expanding)
        sizePolicy.setHorizontalStretch(0)
        sizePolicy.setVerticalStretch(0)
        sizePolicy.setHeightForWidth(self.treeview.sizePolicy().hasHeightForWidth())
        self.treeview.setSizePolicy(sizePolicy)
        self.treeview.setMinimumSize(QtCore.QSize(75, 0))
        self.treeview.setMaximumSize(QtCore.QSize(16777215, 16777215))
        self.treeview.setSizeIncrement(QtCore.QSize(100, 0))
        self.treeview.setBaseSize(QtCore.QSize(300, 0))
        self.treeview.setObjectName(_fromUtf8("treeview"))
        self.verticalLayout.addWidget(self.treeview)
        self.horizontalLayout_3 = QtGui.QHBoxLayout()
        self.horizontalLayout_3.setSizeConstraint(QtGui.QLayout.SetDefaultConstraint)
        self.horizontalLayout_3.setObjectName(_fromUtf8("horizontalLayout_3"))
        self.btnRunR = QtGui.QPushButton(self.widget)
        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
        sizePolicy.setHorizontalStretch(0)
        sizePolicy.setVerticalStretch(0)
        sizePolicy.setHeightForWidth(self.btnRunR.sizePolicy().hasHeightForWidth())
        self.btnRunR.setSizePolicy(sizePolicy)
        self.btnRunR.setObjectName(_fromUtf8("btnRunR"))
#        self.horizontalLayout_3.addWidget(self.btnRunR)

        self.label = QtGui.QLabel(self.widget)
        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Preferred)
        sizePolicy.setHorizontalStretch(0)
        sizePolicy.setVerticalStretch(0)
        sizePolicy.setHeightForWidth(self.label.sizePolicy().hasHeightForWidth())
        self.label.setSizePolicy(sizePolicy)
        self.label.setObjectName(_fromUtf8("label"))
        self.horizontalLayout_3.addWidget(self.label)
        self.lineEdit = QtGui.QLineEdit(self.widget)        
            
        self.lineEdit.setText(_fromUtf8(str(self.kwargs['minCor'])))
        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
        sizePolicy.setHorizontalStretch(0)
        sizePolicy.setVerticalStretch(0)
        sizePolicy.setHeightForWidth(self.lineEdit.sizePolicy().hasHeightForWidth())
        self.lineEdit.setSizePolicy(sizePolicy)
        self.lineEdit.setMaximumSize(QtCore.QSize(75, 16777215))
        self.lineEdit.setObjectName(_fromUtf8("lineEdit"))
        self.horizontalLayout_3.addWidget(self.lineEdit)
        spacerItem = QtGui.QSpacerItem(10, 0, QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
        self.horizontalLayout_3.addItem(spacerItem)
        self.numPlots = QtGui.QLineEdit(self.widget)
        self.numPlots.setText(_fromUtf8(str(self.kwargs['numPlots'])))
        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
        sizePolicy.setHorizontalStretch(0)
        sizePolicy.setVerticalStretch(0)
        sizePolicy.setHeightForWidth(self.lineEdit.sizePolicy().hasHeightForWidth())
        
        self.horizontalLayout_6 = QtGui.QHBoxLayout()
        self.horizontalLayout_6.setSpacing(5)
        self.horizontalLayout_6.setMargin(5)
        self.numPlots.setSizePolicy(sizePolicy)
        self.numPlots.setMaximumSize(QtCore.QSize(75, 16777215))
        self.numPlots.setObjectName(_fromUtf8("numPlots"))
        self.numPlotsLabel = QtGui.QLabel(self.widget)
        self.numPlotsLabel.setSizePolicy(sizePolicy)
        self.numPlotsLabel.setObjectName(_fromUtf8("numPlotsLabel"))
        self.horizontalLayout_6.addWidget(self.numPlotsLabel)
        self.horizontalLayout_6.addWidget(self.numPlots)
        
        
        self.chkPresence = QtGui.QCheckBox(self.widget)
        self.chkPresence.setChecked(True)
        self.chkPresence.setText(_fromUtf8("Include presence/count points"))
        self.chkPresence.setObjectName(_fromUtf8("chkPresence"))
        self.verticalLayout.addWidget(self.chkPresence)
        self.chkAbsence = QtGui.QCheckBox(self.widget)
        self.chkAbsence.setChecked(True)
        self.chkAbsence.setText(_fromUtf8("Include absence points"))
        self.chkAbsence.setObjectName(_fromUtf8("chkAbsence"))
        self.verticalLayout.addWidget(self.chkAbsence)
        self.chkBackground = QtGui.QCheckBox(self.widget)
        self.chkBackground.setChecked(True)
        self.chkBackground.setText(_fromUtf8("Include background points"))
        self.chkBackground.setObjectName(_fromUtf8("chkBackground"))
        self.verticalLayout.addWidget(self.chkBackground)
        
        self.verticalLayout.addLayout(self.horizontalLayout_3)
        self.verticalLayout.addLayout(self.horizontalLayout_6)
        self.horizontalLayout_5 = QtGui.QHBoxLayout()
        self.horizontalLayout_5.addWidget(self.btnRunR)
        self.verticalLayout.addLayout(self.horizontalLayout_5)
        
        
        self.view = utils.InteractiveQGraphicsView(self)
        
        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
        sizePolicy.setHorizontalStretch(4)
        sizePolicy.setVerticalStretch(0)
        #sizePolicy.setHeightForWidth(self.view.sizePolicy().hasHeightForWidth())
        self.view.setSizePolicy(sizePolicy)
        self.view.setResizeAnchor(QtGui.QGraphicsView.AnchorUnderMouse)
        self.view.setObjectName(_fromUtf8("view"))
        
        self.splitter.addWidget(self.view)
        
        self.verticalLayout_3.addWidget(self.splitter)
        self.horizontalLayout = QtGui.QHBoxLayout()
        self.horizontalLayout.setContentsMargins(-1, 3, -1, 3)
        self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
        self.btnOK = QtGui.QPushButton()
        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
        sizePolicy.setHorizontalStretch(0)
        sizePolicy.setVerticalStretch(0)
        sizePolicy.setHeightForWidth(self.btnOK.sizePolicy().hasHeightForWidth())
        self.btnOK.setSizePolicy(sizePolicy)
        self.btnOK.setBaseSize(QtCore.QSize(100, 0))
        self.btnOK.setToolTip(_fromUtf8(""))
        self.btnOK.setObjectName(_fromUtf8("btnOK"))
        self.horizontalLayout.addWidget(self.btnOK)
        self.btnCancel = QtGui.QPushButton()
        sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
        sizePolicy.setHorizontalStretch(0)
        sizePolicy.setVerticalStretch(0)
        sizePolicy.setHeightForWidth(self.btnCancel.sizePolicy().hasHeightForWidth())
        self.btnCancel.setSizePolicy(sizePolicy)
        self.btnCancel.setBaseSize(QtCore.QSize(100, 0))
        self.btnCancel.setObjectName(_fromUtf8("btnCancel"))
        self.horizontalLayout.addWidget(self.btnCancel)
        self.verticalLayout_3.addLayout(self.horizontalLayout)
        self.horizontalLayout_4.addLayout(self.verticalLayout_3)

        self.setWindowTitle(_fromUtf8("Covariate Correlation viewer"))
        self.label_2.setText(_fromUtf8("Covariates"))
        self.btnRunR.setText(_fromUtf8("Update"))
        self.label.setText(_fromUtf8("Threshold"))
        self.numPlotsLabel.setText(_fromUtf8("Number of Plots"))
        self.btnOK.setText(_fromUtf8("OK"))
        self.btnCancel.setText(_fromUtf8("Cancel"))
        self.resize(1100, 800)
        self.view.resize(750, 750)
        
        ##End  autogenerated code from QtDesigner
        
        layout.addLayout(self.horizontalLayout_4)
        
        self.btnCancel.setShortcut('Esc')
        self.connect(self.btnOK, QtCore.SIGNAL('clicked(bool)'),
                     self.okTriggered)
        self.connect(self.btnCancel, QtCore.SIGNAL('clicked(bool)'),
                     self.cancel)
        self.connect(self.btnRunR, QtCore.SIGNAL('clicked(bool)'),
                     self.update_pairs_plot)
        self.connect(self.lineEdit, QtCore.SIGNAL('textChanged(QString)'),
                     self.thresholdEdit)
        self.connect(self.numPlots, QtCore.SIGNAL('textChanged(QString)'),
             self.numPlotsEdit)
        
        self.connect(self.treeview, QtCore.SIGNAL('itemDoubleClicked(QTreeWidgetItem*, int)'), self.on_item_doublclick)

        
        
        #code to populate the treeview with the contents of our MDS
        self.PopulateTreeview()
        
        self.setLayout(layout)
        self.repaint()

        #code to add in pictureviewer stuff
        outputPic = self.make_new_pairs_plot(self.inputMDS)
        self.view.load_picture(outputPic)
        
        
    def on_item_doublclick(self, item, column):
        QtGui.QApplication.setOverrideCursor(QtGui.QCursor(QtCore.Qt.WaitCursor))
        output_dir = os.path.join(self.outputDir, "PredictorInspections")
        if not os.path.exists(output_dir):
            os.makedirs(output_dir)
            
        outputPic = self.makeNewCovariatePlot(output_dir, str(item.text(0)))
        QtGui.QApplication.restoreOverrideCursor()
        self.popup = QtGui.QDialog()
#        self.popup.setBaseSize(1200, 1200)
        size = 800
        self.popup.resize(size, size)
        
        viewWindow = utils.InteractiveQGraphicsView(self.popup)
        viewWindow.resize(size, size)
        layout = QtGui.QVBoxLayout()
        layout.addWidget(viewWindow)
        self.popup.setLayout(layout)
        viewWindow.load_picture(outputPic)
        viewWindow.view_current()
        
        retVal = self.popup.exec_()
        
        
    def okTriggered(self):
        self.SaveMDSFromTreeview()
        self.done(0)

    def cancel(self):
        self.done(1)
        
    def thresholdEdit(self):
        try:
            self.kwargs['minCor'] = float(str(self.lineEdit.text()))
        except ValueError:
            pass
     
    def numPlotsEdit(self):
        try:
            self.kwargs['numPlots'] = int(str(self.numPlots.text()))
        except ValueError:
            pass   
        
    
    def PopulateTreeview(self):
        ''' Reads in the input MDS and populates the treeview widget
        with the items in covariate columns.  
        Sets the check state to be the same as the 0/1 include flag.
        '''
        writetolog("    PopulateTreeview inputMDS = " + self.inputMDS, False, False)
        
#        self.treeview.setColumnCount(2)
        #If an outputMDS already exists then the user has run this module before.
        #We need to pull and apply their previous selections from that output file
        csvfile = open(self.inputMDS, "r")
        #print "MDS", self.inputMDS
        reader = csv.reader(csvfile)
        header = reader.next() #store the header
        header2 = reader.next() #the 2nd line of the mds with use/don't use
        header3 = reader.next() #the 3rd line of the mds with the path
        
        self.responseCol = header[2]
        
        headerList = []
        n = 0
        for i in range(0, len(header)):
            headerList.append([header[i], header2[i], header3[i]])
        
        noncovariate_columns = ['Split', 'EvalSplit']
        for item in headerList[3:]:
            if not item[0] in noncovariate_columns:
                child_item = QtGui.QTreeWidgetItem([_fromUtf8(item[0]), "0"])
                child_item.setFlags(QtCore.Qt.ItemIsUserCheckable |
                                QtCore.Qt.ItemIsEnabled)
                checked = True
                if int(item[1]) == 0:
                    checked = False 
                
                if not checked:
                    child_item.setCheckState(0, QtCore.Qt.Unchecked)
                else:
                    child_item.setCheckState(0, QtCore.Qt.Checked)
                
                self.treeview.addTopLevelItem(child_item)
                #self.tree_items[file] = child_item
                n += 1
        csvfile.close()
        #update the tree view label to show how many covariates there are
        self.label_2.setText(_fromUtf8("Covariates   (n=" + str(n) + ")"))

        
    def SaveMDSFromTreeview(self):
        #updates the second header line on the input MDS file 
        #to reflect the checked items in the tree view 
        #and saves the results to the output MDS.
        
        reader = csv.reader(open(self.inputMDS, "r"))
        header = reader.next() #store the header
        header2 = reader.next() #the 2nd line of the mds with use/don't use
        header3 = reader.next() #the 3rd line of the mds with the path
        
        outHeader2 = header2
        outHeader2[2] = self.selection_name    
                  
        treeviewIter = QtGui.QTreeWidgetItemIterator(self.treeview)
        while treeviewIter.value():
            item = treeviewIter.value()
            col_index = header.index(item.text(0))
            if item.checkState(0) == QtCore.Qt.Checked:
                outHeader2[col_index] = "1"
            else:
                outHeader2[col_index] = "0"
            treeviewIter += 1

        oFile = open(self.outputMDS, 'wb')
        writer = csv.writer(oFile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
        writer.writerow(header)
        writer.writerow(outHeader2)
        writer.writerow(header3)
        for row in reader:
            writer.writerow(row)
        oFile.close

    def update_pairs_plot(self):
        self.SaveMDSFromTreeview()
        outputPic = self.make_new_pairs_plot(self.outputMDS)

        self.view.load_picture(outputPic)
        
    def make_new_pairs_plot(self, MDSfile):

        args = {'i':  MDSfile,
                'o': self.displayJPEG,
                'rc': self.responseCol}
        
        checkboxes = [('pres', self.chkPresence),
                      ('absn', self.chkAbsence),
                      ('bgd', self.chkBackground)]
        for arg, checkbox in checkboxes:
            args[arg] = str(checkbox.checkState() == QtCore.Qt.Checked).upper()
        
        kwarg_args = [('p', 'numPlots'),
                      ('m', 'minCor'),
                      ('core', 'corsWithHighest')]
        for arg, kwarg_key in kwarg_args:
            if kwarg_key in self.kwargs:
                args[arg] = str(self.kwargs[kwarg_key])
                
        if os.path.exists(os.path.join(self.outputDir, "Predictor_Correlation.png")):
            os.remove(os.path.join(self.outputDir, "Predictor_Correlation.png"))
            
        utils.run_R_script('PairsExplore.r', args, self.module, new_r_path=self.kwargs['r_path'])
        
        if os.path.exists(os.path.join(self.outputDir, "devinfo.csv")):
            self.loadDeviances()
        
        if os.path.exists(os.path.join(self.displayJPEG)):
            return os.path.join(self.displayJPEG)
        else:
            writetolog("Missing output from R processing: " + self.displayJPEG)
            raise Exception, "Missing output from R processing"
    
    def saveExploreOptions(self, args):
        checkboxes = [('pres', self.chkPresence),
                      ('absn', self.chkAbsence),
                      ('bgd', self.chkBackground)]
        for arg, checkbox in checkboxes:
            args[arg] = str(checkbox.checkState() == QtCore.Qt.Checked).upper()
        
    def loadDeviances(self):
        #store the deviances explained in dev
        devfname = os.path.join(self.outputDir, "devinfo.csv")
        devcsv = open(devfname)
        devreader = csv.reader(devcsv)
        header = devreader.next()
        for line in devreader:
            try:
                deviance = "%.1f" %float(line[1])
                deviance = deviance.rjust(7)
                try:
                    item = self.treeview.findItems(_fromUtf8(line[0]), QtCore.Qt.MatchFlags())
                    item[0].setData(1, 0, deviance)
                except:
                    print "Problem encountered with item: ", line[0]
            except:
                print "problem loading deviances"
        del devcsv
        self.treeview.sortByColumn(1)

    def makeNewCovariatePlot(self, output_dir, covariate):
        output_fname = os.path.join(output_dir, covariate + ".png")
        
        args = {"i":self.inputMDS, 
            "o":output_dir, 
            "rc":self.responseCol,
            "p":covariate}
        self.saveExploreOptions(args)
            
        if os.path.exists(output_fname):
            os.remove(output_fname)
            
        utils.run_R_script('Predictor.inspection.r', args)
        
        if os.path.exists(output_fname):
            return output_fname
        else:
            writetolog("Missing output from R processing: " + self.displayJPEG)
            raise Exception, "Missing output from R processing"
        
    def closeEvent(self, event):
        self.cancel()