def openSingleAmphitriteDataFile(self, event, textCtrl):
"""Open amphitrite data file ('.a'), using path form textCtrl.
:parameter textCtrl: Data file textCtrl, usually self.textCtrlFile1
"""
dlg = wx.FileDialog(self,
message='Select Amphitrite Data File',
defaultFile=self.settings.defaultDirectory,
wildcard='Amphitrite data file (*.a)|*.a',
style=wx.OPEN | wx.CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
self.settings.defaultDirectory = os.path.dirname(path)
textCtrl.SetValue(path)
# deal with data
dataList = utils.unPickleAmphitriteProject(path)
if dataList:
imOb = Im()
imOb.setDataFromAmphiExtract(dataList)
imOb.normalisationBpi()
imOb.generateMassSpectrum()
imOb.massSpectrum.normalisationBpi()
return imOb
else:
message = 'Error in amphitrite file: %s' % path
gf.warningDialog(message)
dlg.Destroy()
def openSingleAmphitriteDataFile(self,event,textCtrl):
"""Open amphitrite data file ('.a'), using path form textCtrl.
:parameter textCtrl: Data file textCtrl, usually self.textCtrlFile1
"""
dlg = wx.FileDialog(
self,message = 'Select Amphitrite Data File',
defaultFile = self.settings.defaultDirectory,
wildcard = 'Amphitrite data file (*.a)|*.a',
style=wx.OPEN | wx.CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
self.settings.defaultDirectory = os.path.dirname(path)
textCtrl.SetValue(path)
# deal with data
dataList = utils.unPickleAmphitriteProject(path)
if dataList:
imOb = Im()
imOb.setDataFromAmphiExtract(dataList)
imOb.normalisationBpi()
imOb.generateMassSpectrum()
imOb.massSpectrum.normalisationBpi()
return imOb
else:
message = 'Error in amphitrite file: %s' %path
gf.warningDialog(message)
dlg.Destroy()
def eventButtonLoad(self, event): # wxGlade: AtroposGui.<event_handler>
"""Open mass spectrum and display it. Takes information from grain and openFilePath()."""
path = self.textCtrlOpen.GetValue()
self.settings.openFilePath = path
if path[-4:] == '.txt':
# textfile only
grain = self.textCtrlGrain.GetValue()
success = 0
if grain != '':
try:
grain = float(self.textCtrlGrain.GetValue())
success = 1
except:
print 'Grain value not a float'
if success:
self.msPanel.loadTextFile(path, grain)
else:
self.msPanel.loadTextFile(path)
elif path[-2:] == '.a':
self.msPanel.loadAmphiFile(path)
else:
message = \
'''
Problem with file extension:
%s
Aborting...
''' %path
gf.warningDialog(message)
def eventButtonLoad(self, event): # wxGlade: AtroposGui.<event_handler>
"""Open mass spectrum and display it. Takes information from grain and openFilePath()."""
path = self.textCtrlOpen.GetValue()
self.settings.openFilePath = path
if path[-4:] == '.txt':
# textfile only
grain = self.textCtrlGrain.GetValue()
success = 0
if grain != '':
try: grain = float(self.textCtrlGrain.GetValue()) ; success = 1
except: print 'Grain value not a float'
if success:
self.msPanel.loadTextFile(path,grain)
else:
self.msPanel.loadTextFile(path)
elif path[-2:] == '.a':
self.msPanel.loadAmphiFile(path)
else:
message = \
'''
Problem with file extension:
%s
Aborting...
''' %path
gf.warningDialog(message)
def loadTxtData(self,filenames):
"""Load data from spectrum list data files and store the
valid filenames in self.txtFilenames.
:parameter filenames: List of absolute paths
"""
toRemove = []
for fn in filenames:
if not fn in self.loadedTxtFiles.keys():
try:
msOb = MassSpectrum.MassSpectrum()
msOb.readFile(fn)
self.loadedTxtFiles[fn] = msOb
self.massSpectra[fn] = msOb
print 'Sucessfully Added: %s' %fn
# save the filename
self.txtFilenames.append(fn)
self.msFitApplied[fn] = False
except:
toRemove.append(fn)
if len(toRemove):
if len(toRemove) == 1:
message = 'Incorrect file format for: %s' %fn
else:
s = ['\n%s' %fn for fn in toRemove]
s = ''.join(s)
message = 'Incorrect file format for:'+s
gf.warningDialog(message)
return toRemove
def loadTxtData(self, filenames):
"""Load data from spectrum list data files and store the
valid filenames in self.txtFilenames.
:parameter filenames: List of absolute paths
"""
toRemove = []
for fn in filenames:
if not fn in self.loadedTxtFiles.keys():
try:
msOb = MassSpectrum.MassSpectrum()
msOb.readFile(fn)
self.loadedTxtFiles[fn] = msOb
self.massSpectra[fn] = msOb
print 'Sucessfully Added: %s' % fn
# save the filename
self.txtFilenames.append(fn)
self.msFitApplied[fn] = False
except:
toRemove.append(fn)
if len(toRemove):
if len(toRemove) == 1:
message = 'Incorrect file format for: %s' % fn
else:
s = ['\n%s' % fn for fn in toRemove]
s = ''.join(s)
message = 'Incorrect file format for:' + s
gf.warningDialog(message)
return toRemove
def setCalibration(self,filename):
"""Open the amphitrite IM calibration object.
:parameter filename: Absolute path to pickled imClasses.Calibration() object
"""
import imClasses.Calibration
try:
self.calibrationOb = pickle.load(open(filename,'rb'))
except:
message = 'Something wrong with calibration file!'
gf.warningDialog(message)
def setCalibration(self, path):
"""Load pickled calibration object.
:parameter path: Absolute path to imClasses.Calibration() object
"""
import imClasses.Calibration
try:
self.calibrationOb = pickle.load(open(path, 'rb'))
except:
message = 'Something wrong with calibration file!'
gf.warningDialog(message)
def eventTextCtrlWidthR(self, event): # wxGlade: SpectralAveragingGui.<event_handler>
"""Set the right peak FWHM multiplier for extracting arrival times.
"""
val = gf.checkIfNumberTextCtrl(self.textCtrlWidthR)
if type(val).__name__ != 'str':
self.settings.setWidthR(val)
else:
message = 'Please only enter numbers in this box!'
gf.warningDialog(message)
self.textCtrlWidthR.SetValue(str(self.settings.widthR))
def setCalibration(self, filename):
"""Open the amphitrite IM calibration object.
:parameter filename: Absolute path to pickled imClasses.Calibration() object
"""
import imClasses.Calibration
try:
self.calibrationOb = pickle.load(open(filename, 'rb'))
except:
message = 'Something wrong with calibration file!'
gf.warningDialog(message)
def setCalibration(self,path):
"""Load pickled calibration object.
:parameter path: Absolute path to imClasses.Calibration() object
"""
import imClasses.Calibration
try:
self.calibrationOb = pickle.load(open(path,'rb'))
except:
message = 'Something wrong with calibration file!'
gf.warningDialog(message)
def setManualMass(self,massText):
"""For use with plotting theoretical charge state m/z values.
:parameter massText: Mass of species as text or number
"""
try:
self.gui.msPanel.temporaryTheoMzs(massText)
except:
event.Veto()
gf.warningDialog('Only enter numbers here!')
def eventTextCtrlLimit(self, event): # wxGlade: ContourGui.<event_handler>
"""Enter the limit for ignoring peaks when peak picking for "Show peak
tops" check box. Value is given as percentage of base peak intensity.
"""
val = gf.checkIfNumberTextCtrl(self.textCtrlLimit)
if type(val).__name__ == 'str':
message = 'Please only enter numbers in this box!'
gf.warningDialog(message)
self.textCtrlLimit.SetValue(self.settings.limit) # (its left as a string)
else:
self.settings.limit = self.textCtrlLimit.GetValue()
def eventTextCtrlWidthR(
self, event): # wxGlade: SpectralAveragingGui.<event_handler>
"""Set the right peak FWHM multiplier for extracting arrival times.
"""
val = gf.checkIfNumberTextCtrl(self.textCtrlWidthR)
if type(val).__name__ != 'str':
self.settings.setWidthR(val)
else:
message = 'Please only enter numbers in this box!'
gf.warningDialog(message)
self.textCtrlWidthR.SetValue(str(self.settings.widthR))
def eventTextCtrlVmax(self, event): # wxGlade: ContourGui.<event_handler>
"""The value used for the maximum color saturation value.
"""
val = gf.checkIfNumberTextCtrl(self.textCtrlVmax)
if type(val).__name__ != 'str':
self.plotPanel.setVmax(val)
self.plotPanel.refresh_plot()
else:
message = 'Please only enter numbers in this box!'
gf.warningDialog(message)
self.textCtrlVmax.SetValue(str(self.plotPanel.vmax))
def eventTextCtrlVmax(self, event): # wxGlade: ContourGui.<event_handler>
"""The value used for the maximum color saturation value.
"""
val = gf.checkIfNumberTextCtrl(self.textCtrlVmax)
if type(val).__name__ != 'str':
self.plotPanel.setVmax(val)
self.plotPanel.refresh_plot()
else:
message = 'Please only enter numbers in this box!'
gf.warningDialog(message)
self.textCtrlVmax.SetValue(str(self.plotPanel.vmax))
def eventTextCtrlLimit(self, event): # wxGlade: ContourGui.<event_handler>
"""Enter the limit for ignoring peaks when peak picking for "Show peak
tops" check box. Value is given as percentage of base peak intensity.
"""
val = gf.checkIfNumberTextCtrl(self.textCtrlLimit)
if type(val).__name__ == 'str':
message = 'Please only enter numbers in this box!'
gf.warningDialog(message)
self.textCtrlLimit.SetValue(
self.settings.limit) # (its left as a string)
else:
self.settings.limit = self.textCtrlLimit.GetValue()
def eventProcess(self, event): # wxGlade: ImProcessorGui.<event_handler>
"""Convert the selected Synapt data files into Amphitrite
files. (Process button event.)
"""
# TODO(gns) - important sounding comment below here, check what its about
## NEED TO CHECK GRAIN AND OTHER TEXT BOXES
selected = self._getSelectedItemsListCtrl()
if not len(selected):
message = 'Please select one or more files and try again'
gf.warningDialog(message)
else:
grain = self._processGrain()
self.settings.extract_rawfiles(selected, grain, self)
def OnEndLabelEdit(self,event):
"""Function for editing the value labels for each of the
data files.
"""
val = event.GetText()
message = 'Only enter numerical values here'
if len(val):
if utils.isNumber(val):
self.listCtrl.SetItemText(event.GetIndex(),val)
self.updateUnitValues()
self.plotPanel.refresh_plot()
else:
gf.warningDialog(message)
event.Veto()
def _displayPeaks(self):
"""Show peaks found using first derivative and those added manually."""
limit = self.settings.getLimit()
numberOfPeaksFound = self.msPanel.plotMsWithGpeaks(limit)
if numberOfPeaksFound != None:
message = \
'''Over 2000 peaks found (%d)
Please reduce by doing one of the following:
+ Increase smoothing
+ Increase peak identification limit
+ Increase the grain of spectrum (text input only)
''' %numberOfPeaksFound
gf.warningDialog(message)
self.radioBoxDisplay.SetSelection(0)
def _displayPeaks(self):
"""Show peaks found using first derivative and those added manually."""
limit = self.settings.getLimit()
numberOfPeaksFound = self.msPanel.plotMsWithGpeaks(limit)
if numberOfPeaksFound != None:
message = \
'''Over 2000 peaks found (%d)
Please reduce by doing one of the following:
+ Increase smoothing
+ Increase peak identification limit
+ Increase the grain of spectrum (text input only)
''' %numberOfPeaksFound
gf.warningDialog(message)
self.radioBoxDisplay.SetSelection(0)
def eventTextCtrlGrain(self,
event): # wxGlade: ImProcessorGui.<event_handler>
"""Set the grain of the m/z binning when converting the data files.
"""
val = event.GetString()
if val != '':
try:
val = float(val)
if val % 1 == 0:
val = int(val)
self.grainValue = val
except:
message = 'Please only enter numbers!'
gf.warningDialog(message)
self.textCtrlGrain.SetValue(str(self.grainValue))
def eventTextCtrlWidthR(self, event): # wxGlade: ContourGui.<event_handler>
"""Set the peak width (FWHM) multiplier to use for above the peak centre.
(Is used to change the m/z window which is used for a charge state peak.)
"""
val = gf.checkIfNumberTextCtrl(self.textCtrlWidthR)
species = self.choiceSpecies.GetStringSelection()
if type(val).__name__ != 'str':
if species != 'Apply to all':
self.settings.setWidthR(val,species)
else:
for sp in self.settings.widthR.keys():
self.settings.setWidthR(val,sp)
self.plotPanel.refresh_plot()
else:
message = 'Please only enter numbers in this box!'
gf.warningDialog(message)
self.textCtrlWidthR.SetValue(str(self.settings.widthR[species]))
def eventTextCtrlWidthR(self,
event): # wxGlade: ContourGui.<event_handler>
"""Set the peak width (FWHM) multiplier to use for above the peak centre.
(Is used to change the m/z window which is used for a charge state peak.)
"""
val = gf.checkIfNumberTextCtrl(self.textCtrlWidthR)
species = self.choiceSpecies.GetStringSelection()
if type(val).__name__ != 'str':
if species != 'Apply to all':
self.settings.setWidthR(val, species)
else:
for sp in self.settings.widthR.keys():
self.settings.setWidthR(val, sp)
self.plotPanel.refresh_plot()
else:
message = 'Please only enter numbers in this box!'
gf.warningDialog(message)
self.textCtrlWidthR.SetValue(str(self.settings.widthR[species]))
def OnEndLabelEdit(self, event):
"""Editing CCS value of a selected conformation entry in the ListCtrl.
"""
newVal = event.GetText()
i = event.GetIndex()
if utils.isNumber(newVal):
newVal = float(newVal)
self.conformations[i] = newVal
self.updateListCtrl()
self.plotPanel.refresh_plot()
else:
if not newVal == '':
message = 'Only enter a numerical value here!'
gf.warningDialog(message)
event.Veto()
else:
del self.conformations[i]
self.updateListCtrl()
def eventButtonExportTextFile(self, event): # wxGlade: SpectralAveragingGui.<event_handler>
"""Export a text file spectrum list of the averaged mass spectrum.
"""
if len(self.settings.massSpectra):
dlg = wx.FileDialog(
self, message="Save file as ...",
defaultDir=self.settings.defaultDirectory,
defaultFile="",
wildcard='Text file (*.txt)|*.txt| All files (*.*)|*.*',
style=wx.SAVE
)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
self.settings.exportMsTxtFile(path)
self.settings.defaultDirectory = os.path.dirname(path)
dlg.Destroy()
else:
message = 'Load files before exporting!'
gf.warningDialog(message)
def OnEndLabelEdit(self,event):
"""Editing CCS value of a selected conformation entry in the ListCtrl.
"""
newVal = event.GetText()
i = event.GetIndex()
if utils.isNumber(newVal):
newVal = float(newVal)
self.conformations[i] = newVal
self.updateListCtrl()
self.plotPanel.refresh_plot()
else:
if not newVal == '':
message = 'Only enter a numerical value here!'
gf.warningDialog(message)
event.Veto()
else:
del self.conformations[i]
self.updateListCtrl()
def eventButtonExportTextFile(
self, event): # wxGlade: SpectralAveragingGui.<event_handler>
"""Export a text file spectrum list of the averaged mass spectrum.
"""
if len(self.settings.massSpectra):
dlg = wx.FileDialog(
self,
message="Save file as ...",
defaultDir=self.settings.defaultDirectory,
defaultFile="",
wildcard='Text file (*.txt)|*.txt| All files (*.*)|*.*',
style=wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
self.settings.exportMsTxtFile(path)
self.settings.defaultDirectory = os.path.dirname(path)
dlg.Destroy()
else:
message = 'Load files before exporting!'
gf.warningDialog(message)
def getOutDirPath(self):
"""Get output directory path. If alternate directory checkbox is selected
get the value from the output directory textCtrl, otherwise return the input
directory.
:returns: Absolute output path
"""
if self.gui.checkboxAlternateDirectory.IsChecked():
dirPath = self.gui.textCtrlAlternateDirectory.GetValue()
if os.path.isdir(dirPath):
return dirPath
else:
message = \
'''
Output directory not found:
%s
Using default directory:
%s
''' %(dirPath,self.inDirPath)
gf.warningDialog(message)
return self.inDirPath
else:
return self.inDirPath
def _processGrain(self):
"""Check that the value for m/z binning widths (grain) is valid.
:returns: grain (float)
"""
grain = self.textCtrlGrain.GetValue()
try:
grain = float(grain)
if grain < 0.5:
# warning message
message = 'Grain spacing too low: %s\n \
Using minimum value (0.5 m/z units)' % grain
dial = wx.MessageDialog(None, message, 'Warning',
wx.OK | wx.ICON_EXCLAMATION)
dial.ShowModal()
# set grain value
grain = 0.5
except:
# warning message
message = 'Non-number used for grain: %s\n \
Using default value (2.0 m/z units)' % grain
gf.warningDialog(message)
# set grain value
grain = 2.0
return grain