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SelectAndTestFinalModel.py
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###############################################################################
##
## Copyright (C) 2010-2012, USGS Fort Collins Science Center.
## All rights reserved.
## Contact: [email protected]
##
## This file is part of the Software for Assisted Habitat Modeling package
## for VisTrails.
##
## "Redistribution and use in source and binary forms, with or without
## modification, are permitted provided that the following conditions are met:
##
## - Redistributions of source code must retain the above copyright notice,
## this list of conditions and the following disclaimer.
## - Redistributions in binary form must reproduce the above copyright
## notice, this list of conditions and the following disclaimer in the
## documentation and/or other materials provided with the distribution.
## - Neither the name of the University of Utah nor the names of its
## contributors may be used to endorse or promote products derived from
## this software without specific prior written permission.
##
## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
##
## Although this program has been used by the U.S. Geological Survey (USGS),
## no warranty, expressed or implied, is made by the USGS or the
## U.S. Government as to the accuracy and functioning of the program and
## related program material nor shall the fact of distribution constitute
## any such warranty, and no responsibility is assumed by the USGS
## in connection therewith.
##
## Any use of trade, firm, or product names is for descriptive purposes only
## and does not imply endorsement by the U.S. Government.
###############################################################################
from PyQt4 import QtCore, QtGui
import csv
import utils
from utils import writetolog
import shutil
import os
import subprocess
import glob
try:
from vistrails.core.modules.vistrails_module import Module
from vistrails.core.system import execute_cmdline
except ImportError:
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 SelectAndTestFinalModel(QtGui.QDialog):
def __init__(self, session_folder, rPath, parent=None):
self.rPath = rPath
self.session_folder = session_folder
self.findModel = FindModelType(session_folder, parent)
self.csv_file = self.findModel.csv_file
self.display_jpeg = self.findModel.jpeg_file
QtGui.QDialog.__init__(self, parent)
layout = QtGui.QVBoxLayout()
self.setWindowFlags(QtCore.Qt.Window)
##begin autogenerated code from QtDesigner
#
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)
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(0, 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)
# spacerItem = QtGui.QSpacerItem(10, 0, QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
# self.horizontalLayout_3.addItem(spacerItem)
#
#
# self.verticalLayout.addLayout(self.horizontalLayout_3)
self.scene = QtGui.QGraphicsScene()
self.view = QtGui.QGraphicsView(self.scene)
#self.view = customGraphicsView(self.scene)
self.view.setDragMode(QtGui.QGraphicsView.ScrollHandDrag)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(4)
sizePolicy.setVerticalStretch(0)
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.chkEvalHoldout = QtGui.QCheckBox()
# self.chkEvalHoldout.setText("Evaluate Hold Out")
# self.chkEvalHoldout.setObjectName(_fromUtf8('chkEvalHoldout'))
# self.lblProduceMaps = QtGui.QLabel()
# self.lblProduceMaps.setText("Produce maps")
# self.chkProb = QtGui.QCheckBox()
# self.chkProb.setText("Probability")
# self.chkProb.setObjectName(_fromUtf8('chkProb'))
# self.chkBin = QtGui.QCheckBox()
# self.chkBin.setText("Binary")
# self.chkBin.setObjectName(_fromUtf8('chkBin'))
# self.chkMess = QtGui.QCheckBox()
# self.chkMess.setText("MESS")
# self.chkMess.setObjectName(_fromUtf8('chkMess'))
self.btnOK = QtGui.QPushButton()
self.btnOK.setObjectName(_fromUtf8("btnOK"))
self.btnOK.setText(_fromUtf8("Evaluate Holdout for Selected Models"))
self.btnCancel = QtGui.QPushButton()
self.btnCancel.setText(_fromUtf8("Cancel"))
self.btnCancel.setObjectName(_fromUtf8("btnCancel"))
# self.horizontalLayout.addWidget(self.chkEvalHoldout)
# self.horizontalLayout.addWidget(self.lblProduceMaps)
# self.horizontalLayout.addWidget(self.chkProb)
# self.horizontalLayout.addWidget(self.chkBin)
# self.horizontalLayout.addWidget(self.chkMess)
self.horizontalLayout.addWidget(self.btnOK)
self.horizontalLayout.addWidget(self.btnCancel)
self.verticalLayout_3.addLayout(self.horizontalLayout)
# 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(""))
# 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.horizontalLayout_4.addLayout(self.verticalLayout_3)
self.setWindowTitle(_fromUtf8("Evaluate Holdout data"))
self.label_2.setText(_fromUtf8("Models"))
# self.btnRunR.setText(_fromUtf8("Run Final Test"))
# self.label.setText(_fromUtf8("Threshold"))
self.resize(1100, 800)
self.view.resize(800, 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.updateROutput)
self.connect(self.view, QtCore.SIGNAL('resize()'),
self.resize)
self.scene.wheelEvent = self.wheel_event
# self.resizeEvent = self.resize_event
#code to populate the treeview with the contents of our MDS
self.PopulateTreeview()
self.setLayout(layout)
self.repaint()
#utils.breakpoint()
#code to add in pictureviewer stuff
# outputPic = self.display_jpeg
# self.setup_view()
self.load_picture(self.display_jpeg)
def okTriggered(self):
self.runR()
#self.done(0)
def cancel(self):
self.done(1)
#raise Exception
# shutil.copyfile(self.inputMDS, self.outputMDS)
def PopulateTreeview(self):
self.treeview.setColumnCount(1)
csvfile = open(self.csv_file, "rb")
#print "MDS", self.inputMDS
reader = csv.reader(csvfile)
header = reader.next() #store the header
lines = []
for row in reader:
lines.append(row)
i = 1
for item in header[1:]:
tooltiptext = ''
for line in lines:
try:
formatedsecond = "%d4" %line[i]
except TypeError:
formatedsecond = line[i]
if line[0] != '':
if line[0][0].lower() == 's':
tooltiptext += line[0] +":\t\t" + formatedsecond +"\n"
else:
tooltiptext += line[0] +":\t" + formatedsecond +"\n"
elif line[0] == '' and line[1] != '':
tooltiptext += "\n" + line[1] +"\n"
child_item = QtGui.QTreeWidgetItem([item,])
child_item.setToolTip(0, _fromUtf8(tooltiptext))
child_item.setFlags(QtCore.Qt.ItemIsUserCheckable |
QtCore.Qt.ItemIsEnabled)
child_item.setCheckState(0, QtCore.Qt.Unchecked)
self.treeview.addTopLevelItem(child_item)
i += 1
csvfile.close()
self.label_2.setText(_fromUtf8("Evaluate holdout for:"))
def runR(self):
#
#create a finalModelEvaluation folder
eval_type = os.path.split(self.findModel.csv_file)[1]
eval_type = os.path.splitext(eval_type)[0]
eval_type = eval_type.replace("AcrossModel", "")
finalFolder = os.path.join(self.session_folder, "FinalModelEvaluation_" + eval_type)
if os.path.exists(finalFolder):
msg = "The folder " + "'FinalModelEvaluation_" + eval_type + "' already exists in this session folder."
msg += "\nThis indicates that the final evaluation metrics have already been calculated."
msg += "\nThese final statistics are only valid for the first time run."
msg += "\nThe previous run of statistics will be displayed now."
msg += "\nIf you really want to re-run these metrics, manually delete the previously created folder 'FinalModelEvaluation_" + eval_type + "'."
msg += "But from a statistical standpoint this is not advised!"
msgbox = QtGui.QMessageBox(self)
msgbox.setText(msg)
msgbox.exec_()
output_disp = os.path.join(finalFolder, "FinalEvaluationBinom.png")
self.load_picture(output_disp)
return None
else:
os.mkdir(finalFolder)
treeviewIter = QtGui.QTreeWidgetItemIterator(self.treeview)
checked_count = 0
while treeviewIter.value():
item = treeviewIter.value()
# col_index = header.index(item.text(0))
if item.checkState(0) == QtCore.Qt.Checked:
checked_count += 1
origWS = os.path.join(self.session_folder, str(item.text(0)), "modelWorkspace")
outfolder = os.path.join(finalFolder, "evaluate_holdout_" + str(item.text(0)))
os.mkdir(outfolder)
args = {"ws":origWS,
"o":outfolder,
'mpt':"FALSE",
'mbt':"FALSE",
'mes':"FALSE",
"pmt":"FALSE"}
utils.run_R_script("EvaluateNewData.r", args)
writetolog("Finished running R for: " + str(item.text(0)) , False, True)
treeviewIter += 1
if checked_count == 1:
utils.run_R_script("EvaluateNewData.r", args)
writetolog("Finished running R for: " + str(item.text(0)) , False, True)
if checked_count == 0:
msg = "No models selected for final evaluation/map production."
msgbox = QtGui.QMessageBox(self)
msgbox.setText(msg)
msgbox.exec_()
else:
output_disp = os.path.join(finalFolder, "FinalEvaluationBinom.png")
self.display_jpeg = output_disp
self.load_picture(output_disp)
# args = "i=" + '"' + MDSfile + '"' + " o=" + '"' + self.displayJPEG + '"' + " m=" + str(self.lineEdit.text())
# args += " rc=" + self.responseCol
#
# if self.chkPresence.checkState() == QtCore.Qt.Checked:
# args += " pres=TRUE"
# else:
# args += " pres=FALSE"
# if self.chkAbsence.checkState() == QtCore.Qt.Checked:
# args += " absn=TRUE"
# else:
# args += " absn=FALSE"
# if self.chkBackground.checkState() == QtCore.Qt.Checked:
# args += " bgd=TRUE"
# else:
# args += " bgd=FALSE"
# command = program + " --vanilla -f " + script + " --args " + args
# writetolog(" " + command, False, False)
# if os.path.exists(os.path.join(self.outputDir, "Predictor_Correlation.jpg")):
# os.remove(os.path.join(self.outputDir, "Predictor_Correlation.jpg"))
#
# utils.runRScript('PairsExplore.r', args)
# p = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
#
# writetolog(" Calculating covariate correlation in r R ")
# ret = p.communicate()
# if ret[1]:
# msg = "An error was encountered in the R script for this module. The R error message is below - \n"
# msg += ret[1]
# writetolog(msg)
# raise Exception, msg
# else:
# writetolog(" Finished in R. ")
# del(ret)
#
# 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 load_picture(self, strPicture):
self.l_pix = QtGui.QPixmap(strPicture)
if self.view.size().width() <= self.view.size().height():
self.max_vsize = self.view.size().width() * 0.95
else:
self.max_vsize = self.view.size().height() * 0.95
self.c_view = self.l_pix.scaled(self.max_vsize, self.max_vsize,
QtCore.Qt.KeepAspectRatio,
QtCore.Qt.SmoothTransformation)
self.view_current()
def view_current(self):
size_img = self.c_view.size()
wth, hgt = QtCore.QSize.width(size_img), QtCore.QSize.height(size_img)
self.scene.clear()
self.scene.setSceneRect(0, 0, wth, hgt)
self.scene.addPixmap(self.c_view)
QtCore.QCoreApplication.processEvents()
def wheel_event (self, event):
numDegrees = event.delta() / 8
numSteps = numDegrees / 15.0
self.zoom(numSteps)
event.accept()
def zoom(self, step):
zoom_step = 0.06
self.scene.clear()
w = self.c_view.size().width()
h = self.c_view.size().height()
w, h = w * (1 + zoom_step*step), h * (1 + zoom_step*step)
self.c_view = self.l_pix.scaled(w, h,
QtCore.Qt.KeepAspectRatio,
QtCore.Qt.SmoothTransformation)
self.view_current()
def closeEvent(self, event):
self.cancel()
def resizeEvent(self, event):
self.load_picture(self.display_jpeg)
class FindModelType():
def __init__(self, session_dir, parent=None):
self.session_dir = session_dir
#check if multiple model types have been run
#options are one of ('Binary' or 'Count')
#and one of ('TestTrain' or '' or 'CV')
globPattern = os.path.join(self.session_dir, "AcrossModel*.csv")
csvOutputs = glob.glob(globPattern)
if len(csvOutputs) > 1:
self.which_type = QtGui.QDialog()
self.which_type.setWindowTitle("Multiple model types found in this Session Folder")
lbl = QtGui.QLabel(self.which_type)
widget_layout = QtGui.QVBoxLayout()
lbl.setText("Multiple model types found in this Session Folder\n\nPlease select the model type you wish to select from and test:\n\n")
widget_layout.addWidget(lbl)
second_layout = QtGui.QVBoxLayout(parent)
for model_type in csvOutputs:
button = QtGui.QPushButton()
buttonText = os.path.split(model_type)[1].replace('.csv', '')
button.setText(buttonText)
button.connection = model_type
button.clicked.connect(self.button_push)
#buttonName.clicked.connect(lambda: self.button_push())
# button.connect(button, QtCore.SIGNAL('clicked(' + model_type + ')'), button_push)
second_layout.addWidget(button)
widget_layout.addLayout(second_layout)
self.which_type.setLayout(widget_layout)
self.which_type.exec_()
else:
self.csv_file = csvOutputs[0]
self.jpeg_file = self.csv_file.replace(".csv", ".png")
def button_push(self):
sender =self.which_type.sender()
self.csv_file = sender.connection
self.which_type.accept()