def OnGetItemInformation(self, itemID, return_list=False):
# get item information
information = {
'start':
str2int(
self.peaklist.GetItem(
itemID, self.config.driftTopColNames['start']).GetText()),
'end':
str2int(
self.peaklist.GetItem(
itemID, self.config.driftTopColNames['end']).GetText()),
'scans':
str2int(
self.peaklist.GetItem(
itemID, self.config.driftTopColNames['end']).GetText()),
'drift_voltage':
str2num(
self.peaklist.GetItem(
itemID,
self.config.driftTopColNames['drift_voltage']).GetText()),
'document':
self.peaklist.GetItem(
itemID, self.config.driftTopColNames['filename']).GetText()
}
if return_list:
start = information['start']
end = information['end']
scans = information['scans']
drift_voltage = information['drift_voltage']
document = information['document']
return start, end, scans, drift_voltage, document
return information
def importConfig(self, fileName=None, e=None):
"""
Imports config from a file
"""
if not os.path.isfile(fileName):
print('not a path')
return
f = open(fileName, 'r')
for line in f:
if len(line.split()) > 1:
if line.startswith("iPolarity "):
self.iPolarity = str(line.split()[1])
if line.startswith("iActivationZone "):
self.iActivationZone = str(line.split()[1])
if line.startswith("iActivationMode "):
self.iActivationMode = str(line.split()[1])
if line.startswith("iSPV "):
self.iSPV = str2int(line.split()[1])
if line.startswith("iScanTime "):
self.iScanTime = str2int(line.split()[1])
if line.startswith("iStartVoltage "):
self.iStartVoltage = str2num(line.split()[1])
if line.startswith("iEndVoltage "):
self.iEndVoltage = str2num(line.split()[1])
if line.startswith("iStepVoltage "):
self.iStepVoltage = str2num(line.split()[1])
if line.startswith("iExponentPerct "):
self.iExponentPerct = str2num(line.split()[1])
if line.startswith("iExponentIncre "):
self.iExponentIncre = str2num(line.split()[1])
if line.startswith("iBoltzmann "):
self.iBoltzmann = str2num(line.split()[1])
# if line.startswith("wrensPath "):
# self.wrensPath = str(line.split(" ")[1::])
# print(self.wrensPath, os.path.isabs(self.wrensPath))
if line.startswith("wrensLinearName "):
self.wrensLinearName = str(line.split()[1])
if line.startswith("wrensExponentName "):
self.wrensExponentName = str(line.split()[1])
if line.startswith("wrensBoltzmannName "):
self.wrensBoltzmannName = str(line.split()[1])
if line.startswith("wrensUserDefinedName "):
self.wrensUserDefinedName = str(line.split()[1])
if line.startswith("wrensResetName "):
self.wrensResetName = str(line.split()[1])
self.wrensLinearPath = "".join(
['"', self.wrensRunnerPath, '" ', self.wrensLinearName, ' "'])
self.wrensExponentPath = "".join(
['"', self.wrensRunnerPath, '" ', self.wrensExponentName, ' "'])
self.wrensBoltzmannPath = "".join(
['"', self.wrensRunnerPath, '" ', self.wrensBoltzmannName, ' "'])
self.wrensUserDefinedPath = "".join(
['"', self.wrensRunnerPath, '" ', self.wrensUserDefinedName, ' "'])
self.wrensResetPath = "".join(
['"', self.wrensRunnerPath, '" ', self.wrensResetName, ' "'])
def onApply(self, evt):
self.onCheckID()
if self.importEvent: return
self.parent.peaklist.CheckItem(self.itemInfo['id'], self.origami_select_value.GetValue())
self.parent.peaklist.SetStringItem(self.itemInfo['id'], self.config.peaklistColNames['charge'],
self.origami_charge_value.GetValue())
self.parent.peaklist.SetStringItem(self.itemInfo['id'], self.config.peaklistColNames['colormap'],
self.origami_colormap_value.GetStringSelection())
self.parent.peaklist.SetStringItem(self.itemInfo['id'], self.config.peaklistColNames['mask'],
num2str(self.origami_mask_value.GetValue()))
self.parent.peaklist.SetStringItem(self.itemInfo['id'], self.config.peaklistColNames['alpha'],
num2str(self.origami_transparency_value.GetValue()))
self.parent.peaklist.SetStringItem(self.itemInfo['id'], self.config.peaklistColNames['method'],
self.origami_method_value.GetStringSelection())
self.parent.peaklist.SetStringItem(self.itemInfo['id'], self.config.peaklistColNames['label'],
self.origami_label_value.GetValue())
if self.itemInfo['parameters'] == None:
self.itemInfo['parameters'] = {}
self.itemInfo['parameters']['firstVoltage'] = str2int(self.origami_startScan_value.GetValue())
self.itemInfo['parameters']['startV'] = str2num(self.origami_startVoltage_value.GetValue())
self.itemInfo['parameters']['endV'] = str2num(self.origami_endVoltage_value.GetValue())
self.itemInfo['parameters']['stepV'] = str2num(self.origami_stepVoltage_value.GetValue())
self.itemInfo['parameters']['spv'] = str2int(self.origami_scansPerVoltage_value.GetValue())
self.itemInfo['parameters']['expIncrement'] = str2num(self.origami_exponentialIncrement_value.GetValue())
self.itemInfo['parameters']['expPercent'] = str2num(self.origami_exponentialPercentage_value.GetValue())
self.itemInfo['parameters']['dx'] = str2num(self.origami_boltzmannOffset_value.GetValue())
# update ion information
self.itemInfo['charge'] = self.origami_charge_value.GetValue()
self.itemInfo['colormap'] = self.origami_colormap_value.GetStringSelection()
self.itemInfo['mask'] = self.origami_mask_value.GetValue()
self.itemInfo['alpha'] = self.origami_transparency_value.GetValue()
self.itemInfo['label'] = self.origami_label_value.GetValue()
self.itemInfo['min_threshold'] = self.origami_min_threshold_value.GetValue()
self.itemInfo['max_threshold'] = self.origami_max_threshold_value.GetValue()
# update ion value
try:
charge = str2int(self.itemInfo['charge'])
ion_centre = (str2num(self.itemInfo['mzStart']) + str2num(self.itemInfo['mzEnd'])) / 2
mw = (ion_centre - self.config.elementalMass['Hydrogen'] * charge) * charge
ion_value = (u"%s ~%.2f Da") % (self.itemInfo['ionName'], mw)
self.origami_ion_value.SetValue(ion_value)
except:
self.origami_ion_value.SetValue(self.itemInfo['ionName'])
self.OnAssignColor(evt=None)
self.parent.onUpdateDocument(itemInfo=self.itemInfo, evt=None)
if evt != None:
evt.Skip()
def onSetupParameters(self, evt):
self.importEvent = True
self.origami_select_value.SetValue(self.itemInfo['select'])
self.origami_filename_value.SetValue(self.itemInfo['document'])
try:
charge = str2int(self.itemInfo['charge'])
ion_centre = (str2num(self.itemInfo['mzStart']) + str2num(self.itemInfo['mzEnd'])) / 2
mw = (ion_centre - self.config.elementalMass['Hydrogen'] * charge) * charge
ion_value = (u"%s ~%.2f Da") % (self.itemInfo['ionName'], mw)
self.origami_ion_value.SetValue(ion_value)
except:
self.origami_ion_value.SetValue(self.itemInfo['ionName'])
self.origami_charge_value.SetValue(str(self.itemInfo['charge']))
self.origami_label_value.SetValue(self.itemInfo['label'])
self.origami_colormap_value.SetStringSelection(self.itemInfo['colormap'])
self.origami_mask_value.SetValue(self.itemInfo['mask'])
self.origami_transparency_value.SetValue(self.itemInfo['alpha'])
self.origami_color_value.SetBackgroundColour(self.itemInfo['color'])
self.origami_min_threshold_value.SetValue(self.itemInfo['min_threshold'])
self.origami_max_threshold_value.SetValue(self.itemInfo['max_threshold'])
if self.itemInfo['parameters'] != None:
self.origami_method_value.SetStringSelection(self.itemInfo['parameters']['method'])
self.origami_startScan_value.SetValue(str(self.itemInfo['parameters'].get('firstVoltage', '')))
self.origami_scansPerVoltage_value.SetValue(str(self.itemInfo['parameters'].get('spv', '')))
self.origami_startVoltage_value.SetValue(str(self.itemInfo['parameters'].get('startV', '')))
self.origami_endVoltage_value.SetValue(str(self.itemInfo['parameters'].get('endV', '')))
self.origami_stepVoltage_value.SetValue(str(self.itemInfo['parameters'].get('stepV', '')))
self.origami_exponentialIncrement_value.SetValue(str(self.itemInfo['parameters'].get('expIncrement', '')))
self.origami_exponentialPercentage_value.SetValue(str(self.itemInfo['parameters'].get('expPercent', '')))
self.origami_boltzmannOffset_value.SetValue(str(self.itemInfo['parameters'].get('dx', '')))
else:
self.origami_startScan_value.SetValue(str(self.config.origami_startScan))
self.origami_scansPerVoltage_value.SetValue(str(self.config.origami_spv))
self.origami_startVoltage_value.SetValue(str(self.config.origami_startVoltage))
self.origami_endVoltage_value.SetValue(str(self.config.origami_endVoltage))
self.origami_stepVoltage_value.SetValue(str(self.config.origami_stepVoltage))
self.origami_exponentialIncrement_value.SetValue(str(self.config.origami_exponentialIncrement))
self.origami_exponentialPercentage_value.SetValue(str(self.config.origami_exponentialPercentage))
self.origami_boltzmannOffset_value.SetValue(str(self.config.origami_boltzmannOffset))
self.origami_method_value.SetStringSelection(self.config.origami_acquisition)
try: self.origami_method_value.SetStringSelection(self.itemInfo['method'])
except: pass
self.enableDisableBoxes(evt=None)
self.importEvent = False
def OnSortByColumn(self, column):
"""
Sort data in peaklist based on pressed column
"""
# Check if it should be reversed
if self.lastColumn == None:
self.lastColumn = column
elif self.lastColumn == column:
if self.reverse == True:
self.reverse = False
else:
self.reverse = True
else:
self.reverse = False
self.lastColumn = column
columns = self.peaklist.GetColumnCount()
rows = self.peaklist.GetItemCount()
tempData = []
# Iterate over row and columns to get data
for row in range(rows):
tempRow = []
for col in range(columns):
item = self.peaklist.GetItem(itemId=row, col=col)
# We want to make sure the first 3 columns are numbers
if col == 0 or col == 1 or col == 2:
itemData = str2num(item.GetText())
if itemData == None: itemData = 0
tempRow.append(itemData)
elif col == 3:
itemData = str2int(item.GetText())
if itemData == None: itemData = 0
tempRow.append(itemData)
else:
tempRow.append(item.GetText())
tempData.append(tempRow)
# Sort data
tempData.sort(key=itemgetter(column), reverse=self.reverse)
# Clear table and reinsert data
self.peaklist.DeleteAllItems()
for row in range(rows):
self.peaklist.Append(tempData[row])
def OnGetItemInformation(self, itemID, return_list=False):
# get item information
information = {
'start':
str2num(
self.peaklist.GetItem(
itemID,
self.config.driftBottomColNames['start']).GetText()),
'end':
str2num(
self.peaklist.GetItem(
itemID, self.config.driftBottomColNames['end']).GetText()),
'intensity':
str2num(
self.peaklist.GetItem(
itemID,
self.config.driftBottomColNames['intensity']).GetText()),
'charge':
str2int(
self.peaklist.GetItem(
itemID,
self.config.driftBottomColNames['charge']).GetText()),
'document':
self.peaklist.GetItem(
itemID, self.config.driftBottomColNames['filename']).GetText()
}
if return_list:
start = information['start']
end = information['end']
intensity = information['intensity']
charge = information['charge']
document = information['document']
return start, end, intensity, charge, document
return information