Push to v2.0.9

stamp/STAMP.py

@@ -23,8 +23,8 @@
 __copyright__ = 'Copyright 2013'
 __credits__ = ['Donovan Parks']
 __license__ = 'GPL3'
-__version__ = '2.0.8'
-__date__ = 'August 4, 2014'
+__version__ = '2.0.9'
+__date__ = 'December 5, 2014'
 __maintainer__ = 'Donovan Parks'
 __email__ = 'donovan.parks@gmail.com'
 __status__ = 'Development'
@@ -35,7 +35,7 @@
 import string
 
 import stamp.Dependencies
-from stamp.GUI.plotDlg import PlotDlg # forward reference so py2app recognizes this file is required
+from stamp.GUI.plotDlg import PlotDlg  # forward reference so py2app recognizes this file is required
 
 from PyQt4 import QtGui, QtCore
 
@@ -200,7 +200,7 @@ def __init__(self, preferences, parent=None):
 
  self.metadata = None
 
- #self.loadProfile() # *** For debugging purposes
+ # self.loadProfile() # *** For debugging purposes
 
  def propertiesTabChanged(self, currentIndex):
  self.ui.stackedWidgetViews.setCurrentIndex(currentIndex)
@@ -691,7 +691,7 @@ def group1ColourDlg(self):
  if colour.isValid():
  self.setGroup1Colour(colour)
 
- def setGroup1Colour(self, colour, bUpdatePlot = True):
+ def setGroup1Colour(self, colour, bUpdatePlot=True):
  colourStr = str(colour.red()) + ',' + str(colour.green()) + ',' + str(colour.blue())
  self.ui.btnGroup1Colour.setStyleSheet('* { background-color: rgb(' + colourStr + ') }')
  self.preferences['Group colours'][self.groupProfile.groupName1] = colour
@@ -706,7 +706,7 @@ def group2ColourDlg(self):
  if colour.isValid():
  self.setGroup2Colour(colour)
 
- def setGroup2Colour(self, colour, bUpdatePlot = True):
+ def setGroup2Colour(self, colour, bUpdatePlot=True):
  colourStr = str(colour.red()) + ',' + str(colour.green()) + ',' + str(colour.blue())
  self.ui.btnGroup2Colour.setStyleSheet('* { background-color: rgb(' + colourStr + ') }')
  self.preferences['Group colours'][self.groupProfile.groupName2] = colour
@@ -757,7 +757,7 @@ def loadProfile(self):
  QtGui.QMessageBox.information(self, 'Error reading profile file', errMsg, QtGui.QMessageBox.Warning)
  return
  except:
- QtGui.QMessageBox.information(self, 'Error reading profile file','Unknown parsing error.', QtGui.QMessageBox.Warning)
+ QtGui.QMessageBox.information(self, 'Error reading profile file', 'Unknown parsing error.', QtGui.QMessageBox.Warning)
  return
 
  self.metadata = None
@@ -800,7 +800,7 @@ def loadProfile(self):
  # indicate the hierarchical level of interest has changed
  bGroupLegendVisibility = self.groupLegendDlg.isVisible()
  if platform.system() != 'Windows' and bGroupLegendVisibility:
- self.groupLegendDlg.setVisible(False) # HACK: OS X crashes if this dialog is open when loading data for the first time!
+ self.groupLegendDlg.setVisible(False) # HACK: OS X crashes if this dialog is open when loading data for the first time!
 
  self.multiGroupHierarchicalLevelsChanged()
  self.groupHierarchicalLevelsChanged()
@@ -829,7 +829,7 @@ def populateGroupComboBoxes(self):
 
  def parentLevelChanged(self):
  parentDepth = self.profileTree.getHierarchicalLevelDepth(str(self.ui.cboParentalLevel.currentText()))
- profileDepth= self.profileTree.getHierarchicalLevelDepth(str(self.ui.cboProfileLevel.currentText()))
+ profileDepth = self.profileTree.getHierarchicalLevelDepth(str(self.ui.cboProfileLevel.currentText()))
  if parentDepth >= profileDepth:
  QtGui.QMessageBox.information(self, 'Invalid profile', 'The parent level must be higher in the hierarchy than the profile level.', QtGui.QMessageBox.Warning)
  self.ui.cboParentalLevel.setCurrentIndex(0)
@@ -840,11 +840,11 @@ def parentLevelChanged(self):
 
  def profileLevelChanged(self):
  parentDepth = self.profileTree.getHierarchicalLevelDepth(str(self.ui.cboParentalLevel.currentText()))
- profileDepth= self.profileTree.getHierarchicalLevelDepth(str(self.ui.cboProfileLevel.currentText()))
+ profileDepth = self.profileTree.getHierarchicalLevelDepth(str(self.ui.cboProfileLevel.currentText()))
 
  if profileDepth <= parentDepth:
  QtGui.QMessageBox.information(self, 'Invalid profile', 'The profile level must be deeper in the hierarchy than the parent level.', QtGui.QMessageBox.Warning)
- self.ui.cboProfileLevel.setCurrentIndex(len(self.profileTree.hierarchyHeadings)-1)
+ self.ui.cboProfileLevel.setCurrentIndex(len(self.profileTree.hierarchyHeadings) - 1)
  return
 
  self.sampleHierarchicalLevelsChanged()
@@ -874,7 +874,7 @@ def sampleHierarchicalLevelsChanged(self):
  profileIndex = self.profileTree.hierarchyHeadings.index(profileHeading)
  self.ui.cboSampleHighlightHierarchy.clear()
  self.ui.cboSampleHighlightHierarchy.addItem('None')
- for header in self.profileTree.hierarchyHeadings[0:profileIndex+1]:
+ for header in self.profileTree.hierarchyHeadings[0:profileIndex + 1]:
  self.ui.cboSampleHighlightHierarchy.addItem(header)
  self.ui.cboSampleHighlightHierarchy.setCurrentIndex(0)
 
@@ -911,7 +911,7 @@ def groupHierarchicalLevelsChanged(self):
  profileIndex = self.profileTree.hierarchyHeadings.index(profileHeading)
  self.ui.cboGroupHighlightHierarchy.clear()
  self.ui.cboGroupHighlightHierarchy.addItem('None')
- for header in self.profileTree.hierarchyHeadings[0:profileIndex+1]:
+ for header in self.profileTree.hierarchyHeadings[0:profileIndex + 1]:
  self.ui.cboGroupHighlightHierarchy.addItem(header)
  self.ui.cboGroupHighlightHierarchy.setCurrentIndex(0)
 
@@ -940,7 +940,7 @@ def multiGroupHierarchicalLevelsChanged(self):
  profileIndex = self.profileTree.hierarchyHeadings.index(profileHeading)
  self.ui.cboMultiGroupHighlightHierarchy.clear()
  self.ui.cboMultiGroupHighlightHierarchy.addItem('None')
- for header in self.profileTree.hierarchyHeadings[0:profileIndex+1]:
+ for header in self.profileTree.hierarchyHeadings[0:profileIndex + 1]:
  self.ui.cboMultiGroupHighlightHierarchy.addItem(header)
  self.ui.cboMultiGroupHighlightHierarchy.setCurrentIndex(0)
 
@@ -977,7 +977,7 @@ def groupFeaturesTableUpdate(self):
  self.preferences['Selected group feature'] = ''
 
  self.groupFeatureTable = GenericTable(tableData, ['Feature', 'Diff. between means', 'p-value', 'Corrected p-value', 'Note'], self)
- self.groupFeatureTable.sort(0,QtCore.Qt.AscendingOrder) # start with features in alphabetical order
+ self.groupFeatureTable.sort(0, QtCore.Qt.AscendingOrder)  # start with features in alphabetical order
 
  self.ui.tableGroupFeatures.horizontalHeader().setStretchLastSection(True)
  self.ui.tableGroupFeatures.setModel(self.groupFeatureTable)
@@ -1007,7 +1007,7 @@ def multiGroupFeaturesTableUpdate(self):
  self.preferences['Selected multiple group feature'] = ''
 
  self.multiGroupFeatureTable = GenericTable(tableData, ['Feature', 'Eta-squared', 'p-value', 'Corrected p-value', 'Note'], self)
- self.multiGroupFeatureTable.sort(0,QtCore.Qt.AscendingOrder) # start with features in alphabetical order
+ self.multiGroupFeatureTable.sort(0, QtCore.Qt.AscendingOrder)  # start with features in alphabetical order
 
  self.ui.tableMultiGroupFeatures.horizontalHeader().setStretchLastSection(True)
  self.ui.tableMultiGroupFeatures.setModel(self.multiGroupFeatureTable)
@@ -1045,7 +1045,7 @@ def sampleRunTest(self):
  self.ui.cboUnclassified.currentText())
 
  # show progress of test
- progress = QtGui.QProgressDialog('Running two-sample statistical test...', 'Cancel', 0, len(self.sampleProfile.getFeatures())+1, self)
+ progress = QtGui.QProgressDialog('Running two-sample statistical test...', 'Cancel', 0, len(self.sampleProfile.getFeatures()) + 1, self)
  progress.setWindowTitle('Progress')
  progress.setWindowModality(QtCore.Qt.WindowModal)
  progress.setVisible(True)
@@ -1093,7 +1093,7 @@ def groupRunTest(self):
  self.setGroup2Colour(self.preferences['All other samples colour'])
 
  # show progress of test
- progress = QtGui.QProgressDialog('Running two-group statistical test...', 'Cancel', 0, len(self.groupProfile.getFeatures())+1, self)
+ progress = QtGui.QProgressDialog('Running two-group statistical test...', 'Cancel', 0, len(self.groupProfile.getFeatures()) + 1, self)
  progress.setWindowTitle('Progress')
  progress.setWindowModality(QtCore.Qt.WindowModal)
  progress.setVisible(True)
@@ -1133,7 +1133,7 @@ def multiGroupRunTest(self):
 
  if len(self.multiGroupProfile.activeGroupNames) >= 2:
  # show progress of test
- progress = QtGui.QProgressDialog('Running multiple groups statistical test...', 'Cancel', 0, len(self.multiGroupProfile.getFeatures())+1, self)
+ progress = QtGui.QProgressDialog('Running multiple groups statistical test...', 'Cancel', 0, len(self.multiGroupProfile.getFeatures()) + 1, self)
  progress.setWindowTitle('Progress')
  progress.setWindowModality(QtCore.Qt.WindowModal)
  progress.setVisible(True)
@@ -1558,7 +1558,7 @@ def sampleHighlightHierarchyChanged(self):
  featureStrList.append(feature)
 
  self.ui.cboSampleHighlightFeature.clear()
- self.ui.cboSampleHighlightFeature.insertItems(len(featureStrList),featureStrList)
+ self.ui.cboSampleHighlightFeature.insertItems(len(featureStrList), featureStrList)
  self.ui.cboSampleHighlightFeature.setCurrentIndex(0)
 
  self.ui.cboSampleHighlightFeature.adjustSize()
@@ -1586,7 +1586,7 @@ def groupHighlightHierarchyChanged(self):
  featureStrList.append(feature)
 
  self.ui.cboGroupHighlightFeature.clear()
- self.ui.cboGroupHighlightFeature.insertItems(len(featureStrList),featureStrList)
+ self.ui.cboGroupHighlightFeature.insertItems(len(featureStrList), featureStrList)
  self.ui.cboGroupHighlightFeature.setCurrentIndex(0)
 
  self.ui.cboGroupHighlightFeature.adjustSize()
@@ -1614,7 +1614,7 @@ def multiGroupHighlightHierarchyChanged(self):
  featureStrList.append(feature)
 
  self.ui.cboMultiGroupHighlightFeature.clear()
- self.ui.cboMultiGroupHighlightFeature.insertItems(len(featureStrList),featureStrList)
+ self.ui.cboMultiGroupHighlightFeature.insertItems(len(featureStrList), featureStrList)
  self.ui.cboMultiGroupHighlightFeature.setCurrentIndex(0)
 
  self.ui.cboMultiGroupHighlightFeature.adjustSize()
@@ -1691,7 +1691,7 @@ def saveImageDlg(self):
  if f != '':
  self.preferences['Last directory'] = f[0:f.lastIndexOf('/')]
  try:
- if f[len(f)-3:len(f)] == 'png' or f[len(f)-3:len(f)] == 'PNG':
+ if f[len(f) - 3:len(f)] == 'png' or f[len(f) - 3:len(f)] == 'PNG':
  dpi, ok = QtGui.QInputDialog.getInteger(self, 'Desired resolution', 'Enter desired resolution (DPI) of image:', 300)
  if ok:
  plotToSave.save(str(f), dpi)
@@ -1760,28 +1760,28 @@ def closeEvent(self, event):
  settings.setValue('Preferences/Minimum reported p-value exponent', self.preferences['Minimum reported p-value exponent'])
 
 def exceptHook(exc_type, exc_value, exc_traceback):
- ## Copyright (c) 2002-2007 Pascal Varet <p.varet@gmail.com>
- ##
- ## Originally part of Spyrit.
+ # # Copyright (c) 2002-2007 Pascal Varet <p.varet@gmail.com>
+ # #
+ # # Originally part of Spyrit.
 
  import traceback
 
- ## KeyboardInterrupt is a special case.
- ## We don't raise the error dialog when it occurs.
- if issubclass( exc_type, KeyboardInterrupt ):
+ # # KeyboardInterrupt is a special case.
+ # # We don't raise the error dialog when it occurs.
+ if issubclass(exc_type, KeyboardInterrupt):
  if qApp():
  qApp().quit()
  return
 
- filename, line, dummy, dummy = traceback.extract_tb( exc_traceback ).pop()
- filename = os.path.basename( filename )
- error = "%s: %s" % ( exc_type.__name__, exc_value)
+ filename, line, dummy, dummy = traceback.extract_tb(exc_traceback).pop()
+ filename = os.path.basename(filename)
+ error = "%s: %s" % (exc_type.__name__, exc_value)
 
  QtGui.QMessageBox.critical(None, "Unknown error...",
  "<center>An error has occured:<br/><br/>"
  + "<b><i>%s</i></b><br/>" % error
- + "It occured at <b>line %d</b> of file <b>%s</b>.<br/>" % ( line, filename )
- + "</center>" )
+ + "It occured at <b>line %d</b> of file <b>%s</b>.<br/>" % (line, filename)
+ + "</center>")
 
 def main():
  # ignore numpy warnings as invalid results are handled within STAMP
@@ -1816,7 +1816,7 @@ def main():
  workingDir = getMainDir()
  preferences['Last directory'] = ''
  if 'STAMP.app/Contents/Resources' in workingDir:
- workingDir = workingDir[0:len(workingDir)-len('/STAMP.app/Contents/Resources')]
+ workingDir = workingDir[0:len(workingDir) - len('/STAMP.app/Contents/Resources')]
  preferences['Last directory'] = workingDir
  os.chdir(workingDir)
 
@@ -1826,23 +1826,23 @@ def main():
  # the program icon is displayed in the taskbar instead of the generic
  # Python icon.
  import ctypes
- myappid = 'beikolab.software.stamp.2' # arbitrary string
+ myappid = 'beikolab.software.stamp.2'  # arbitrary string
  ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
 
  if (platform.system() == 'Windows' and len(sys.argv) == 1) or (platform.system() != 'Windows' and len(sys.argv) <= 2):
  sys.excepthook = exceptHook
  app = QtGui.QApplication(sys.argv)
 
- if(False): # profile code
+ if(False):  # profile code
  import cProfile
  cProfile.run('mainWindow = MainWindow(preferences)', 'profile.txt')
  ##########################################
  ##########################################
  # Use this in python console!
- #import pstats
- #p = pstats.Stats('profile.txt')
- #p.sort_stats('cumulative').print_stats(10)
- #p.sort_stats('time').print_stats(10)
+ # import pstats
+ # p = pstats.Stats('profile.txt')
+ # p.sort_stats('cumulative').print_stats(10)
+ # p.sort_stats('time').print_stats(10)
  ##########################################
  ##########################################
  else: