def _initialize(self):
"""
called in __init__ of msdialogcontroller
"""
settings=QSettings('INRA/INSA', '-'.join([qApp.instance().APPLICATION_NAME_STR,
qApp.instance().VERSION_STR]))
if isinstance(self.view, MSMatchedFilteredDialog):
settings.beginGroup("matchedFilteredDialog")
self.view.lineEdit_2.setText(settings.value("lineEdit_2", "30").toString())
self.view.lineEdit_4.setText(settings.value("lineEdit_4", "2").toString())
self.view.lineEdit_5.setText(settings.value("lineEdit_5", "0.5").toString())
self.view.lineEdit_6.setText(settings.value("lineEdit_6", "3").toString())
self.view.lineEdit_3.setText(settings.value("lineEdit_3", "0.1").toString())
self.view.spinBox.setValue(settings.value("spinBox", 5).toInt()[0])
settings.endGroup()
elif isinstance(self.view, MSCentWaveDialog):
self.view.lineEdit_2.setText("300-3200")
self.view.lineEdit_4.setText("10-22")
self.view.lineEdit_5.setText("1000")
self.view.lineEdit_6.setText("1.2")
self.view.spinBox.setValue(10)
self.view.spinBox_2.setValue(10)
self.view.checkBox.setChecked(True)
self.view.lineEdit_7.setText("0.8")
self.view.lineEdit_8.setText("5")
self.view.lineEdit_9.setText("20")
self.view.lineEdit_10.setText("0.002")
self.view.obiwarp.setChecked(True)
self.view.gb_2.setChecked(False)
self.view.gb_3.setChecked(False)
def startTask(self):
self.getParameters()#update parameters
#self.view.close()#self.closeView()
self.sampleList = self._buildSampleList(creation=self.creation)
if not self.sampleList:
qApp.instance().view.showInformationMessage("Error", "Empty selection")
return
def setModels(self):#, sampleList):
"""
closing function of the process
"""
qApp.instance().view.showInformationMessage("Clustering done", "Clustering Done succesfully !")
qApp.instance().view.tabWidget.setCurrentIndex(2)
def showSSHConnect(self):
self.view.close()
qApp.instance().view.showInformationMessage("Check resources availability",
"Please, check resources of the cluster availability \
in order to select the best queue")
web = MSWebBrowser(self.plateformSite, parent=qApp.instance().view)
qApp.instance().view.addMdiSubWindow(web)
return SSHHandle(self, parent=self.view).show()
def startTask(self):
self.getParameters() #update parameters
#self.view.close()#self.closeView()
self.sampleList = self._buildSampleList(creation=self.creation)
if not self.sampleList:
qApp.instance().view.showInformationMessage(
"Error", "Empty selection")
return
def smooth():
window = dialog.a.value()
order = dialog.b.value()
method = dialog.a_.currentText()
dialog.close()
qApp.instance().undoStack.push(SmoothUndoCommand(QApplication.instance().model,
method, window, order,
"Smoothing #%s"%'1'))
def getStandardItem(self, peak):
m=qApp.instance().view.peakModel
for i in range(qApp.instance().view.peakModel.rowCount()):
it=m.item(i)
if it.text()==self.shortPathFiles(peak.sample.xmlfile):
for i in range(it.rowCount()):
if it.child(i).text()=='/'.join([str(peak.mass()), str(peak.rt)]):
return it.child(i)
def setModels(self): #, sampleList):
"""
closing function of the process
"""
qApp.instance().view.showInformationMessage(
"Clustering done", "Clustering Done succesfully !")
qApp.instance().view.tabWidget.setCurrentIndex(2)
def getStandardItem(self, peak):
m = qApp.instance().view.peakModel
for i in range(qApp.instance().view.peakModel.rowCount()):
it = m.item(i)
if it.text() == self.shortPathFiles(peak.sample.xmlfile):
for i in range(it.rowCount()):
if it.child(i).text() == '/'.join(
[str(peak.mass()), str(peak.rt)]):
return it.child(i)
def notify_data(self, co, uc, svs, dis, ais, evs):
'''
Porpagación a travez de la aplicación de los datos para
que las partes de la UI que necesiten refrescarse lo hagan
tan pronto como puedan. De esta manera no es necesario
acceder a la base de datos.
'''
log.msg('Propagando datos a la GUI de COID: %.2d%.2d' % (co, uc))
qApp.instance().emit(SIGNAL('data_available'), co, uc, svs, dis, ais, evs)
def __init__(self, model, polyDegree, rawData, errorRt, text, parent=None):
QtGui.QUndoCommand.__init__(self, text, parent)
self.qApp = QApplication.instance()
self.model = deepcopy(model)
self.spectraModel = QtGui.QStandardItemModel(qApp.instance().view.spectraModel)
self.peakModel = QtGui.QStandardItemModel(qApp.instance().view.peakModel)
self.clusterModel = QtGui.QStandardItemModel(qApp.instance().view.clusterModel)
self.polyDegree = polyDegree
self.rawData = rawData#boolean value working on raw data ?
self.errorRt = errorRt#if we are working on peaks peakgrouping etc...
def showSSHConnect(self):
self.view.close()
qApp.instance().view.showInformationMessage(
"Check resources availability",
"Please, check resources of the cluster availability \
in order to select the best queue"
)
web = MSWebBrowser(self.plateformSite, parent=qApp.instance().view)
qApp.instance().view.addMdiSubWindow(web)
return SSHHandle(self, parent=self.view).show()
def notify_data(self, co, uc, svs, dis, ais, evs):
'''
Porpagación a travez de la aplicación de los datos para
que las partes de la UI que necesiten refrescarse lo hagan
tan pronto como puedan. De esta manera no es necesario
acceder a la base de datos.
'''
log.msg('Propagando datos a la GUI de COID: %.2d%.2d' % (co, uc))
qApp.instance().emit(SIGNAL('data_available'), co, uc, svs, dis, ais,
evs)
def baselineCorrection(self):
if not self.model:
self.view.showErrorMessage("Error", "No sample available...")
return
string, boolean = QtGui.QInputDialog.getDouble(self.view, "enter a baseline", "quantile value", value=2e3)
if not boolean:
return
qApp.instance().undoStack.push(BaseLineCorrectionCommand(QApplication.instance().model,
string,
"baselineCorrection #%s"%'1'))
def getParameters(self):
"""
will get all the parameters,
make the difference between
the two integration algorithm
"""
settings=QSettings('INRA/INSA', '-'.join([qApp.instance().APPLICATION_NAME_STR,
qApp.instance().VERSION_STR]))
if isinstance(self.view, MSMatchedFilteredDialog):
self.parameters["fwhm"]=str(self.view.lineEdit_2.text())
self.parameters["step"]=str(self.view.lineEdit_3.text())
self.parameters["steps"]=str(self.view.lineEdit_4.text())
self.parameters["mzdiff"]=str(self.view.lineEdit_5.text())
self.parameters["snthresh"]=str(self.view.lineEdit_6.text())
self.parameters["max"]=str(self.view.spinBox.value())
self.parameters["algorithm"]=0
#start change
settings.beginGroup("matchedFilteredDialog")
settings.setValue("lineEdit_2", self.parameters["fwhm"])
settings.setValue("lineEdit_4", self.parameters["steps"])
settings.setValue("lineEdit_5", self.parameters["mzdiff"])
settings.setValue("lineEdit_6", self.parameters["snthresh"])
settings.setValue("lineEdit_3", self.parameters["step"])
settings.setValue("spinBox", int(self.parameters["max"]))
settings.endGroup()
elif isinstance(self.view, MSCentWaveDialog):
self.parameters["scanrange"]=[float(x) for x in self.view.lineEdit_2.text().split('-')]
self.parameters["integrate"]=1 if self.view.lineEdit_3.isChecked()else 0
self.parameters["peakwidth"]=[float(x) for x in self.view.lineEdit_4.text().split('-')]
self.parameters["noise"]=int(self.view.lineEdit_5.text())
self.parameters["mzdiff"]=float(self.view.lineEdit_6.text())
self.parameters["ppm"]=int(self.view.spinBox.value())
self.parameters["snthresh"]=int(self.view.spinBox_2.value())
self.parameters["fitgauss"]=[self.view.checkBox.isChecked()]
self.parameters["algorithm"]=1
#common parameters between the to algorithm
self.parameters['doGrouping']=True if self.view.gb_2.isChecked()else False
if self.parameters['doGrouping']:
self.parameters["minfrac"]=float(self.view.lineEdit_7.text())
self.parameters["bw"]=int(self.view.lineEdit_8.text())
self.parameters["max"]=int(self.view.lineEdit_9.text())
self.parameters["mzwid"]=float(self.view.lineEdit_10.text())
self.parameters["doAlignment"]=True if self.view.gb_3.isChecked() else False
if self.parameters["doAlignment"]:
if self.view.obiwarp.isChecked():
self.parameters["method"] ='obiwarp'
if self.view.loess.isChecked():
self.parameters["method"] ='loess'
def plotPeakSelection(self, index, boolean=False):
"""
Allow to plot peak and peak tables
"""
if not index.isValid():
return
data = index.data().toString().split("/")
prec, rt = float(data[0]), float(data[1])
peaks = self.getElementsToPlot(flags='peak', prec=prec, rt=rt)
pw = MSQtCanvas(peaks,
"peak@%s/%s" % (str(prec), str(rt)),
labels={
'bottom': 'RT(s)',
'left': 'INTENSITY'
},
flags='peak')
QObject.connect(qApp.instance(), SIGNAL('redraw()'), pw.redraw)
title = "peak@%s/%s" % (str(prec), str(rt))
win = self.view.mdiArea.activeSubWindow()
isMax = False
if win is not None and boolean:
isMax = win.isMaximized()
w = win.widget()
#w.connect(w, SIGNAL('destroyed (QObject *)'), self.destroyed)
#w.setParent(None)
sip.delete(w)
del w
win.setWidget(MSView(pw))
#win.close()
else:
self.view.addMdiSubWindow(MSView(pw), title, isMax)
self.view.mdiArea.tileSubWindows()
def plotSelection(self, index, boolean=False):
"""
Allow to plot spectrum
"""
if not index.isValid():
return
chromas = self.getElementsToPlot(flags='spectra', index=index.row())
title = "Spectrum@%s" % str(chromas[0].rtmin)
legend = {'bottom': 'm/z', 'left': 'INTENSITY'}
flags = 'spectra'
#useOpenGL=False
pw = MSQtCanvas(chromas, title, labels=legend,
flags=flags) #, useOpenGL=useOpenGL)
QObject.connect(qApp.instance(), SIGNAL('redraw()'), pw.redraw)
a = self.view.mdiArea.activeSubWindow()
isMax = False
if a is not None and boolean:
isMax = a.isMaximized()
w = a.widget()
#w.connect(w, SIGNAL('destroyed (QObject *)'), self.destroyed)
#w.setParent(None)
#print "parent of w just before elimination", w.parent()
sip.delete(w) #; del w
del w
a.setWidget(pw)
#a.close()
else:
self.view.addMdiSubWindow(pw, title, isMax)
self.view.mdiArea.tileSubWindows()
def startTask(self):
MSDialogController.startTask(self)
self.task = MSIntegrationThread(self.sampleList, **self.parameters)
def begin():
self.view=None
self.task.start()
self.task.exec_()
self.task.begin = begin
#to avoid QObject::killTimers error, wait for the dialog to be deleted
QObject.connect(self.view, SIGNAL('destroyed(QObject *)'), self.task.begin)
QObject.connect(self.task, SIGNAL("started()"),qApp.instance().view.to_indetermined_mode)
QObject.connect(self.task, SIGNAL("finished()"),self.setModels)
QObject.connect(self.task, SIGNAL("finished()"),qApp.instance().view.to_determined_mode)
self.view.close()
def plotClusterSelection(self, index, boolean=False):
"""
Allow to plot peak and cluster tables
"""
if not index.isValid():
return
string = str(index.data().toString())#.model().data(index.parent(), Qt.DisplayRole).toString()
if string in ("fragments/adducts:","isotopic cluster:"):
return
data = string.split('/')
#print data
prec=float(data[0])
rt = float(data[1])
#print prec, rt
peaks=self.getElementsToPlot(flags='peak', prec=prec, rt=rt)
pw = ClusterWidget(peaks, self.view)#MSQtCanvas(peaks, "peak@%s/%s"%(str(prec), str(rt)), labels={'bottom':'RT(s)', 'left':'INTENSITY'}, flags='peak')
QObject.connect(qApp.instance(), SIGNAL('redraw()'), pw.widget.mainWidget.redraw)
title="peak@%s/%s"%(str(prec), str(rt))
win=self.view.mdiArea.activeSubWindow()
isMax=False
if win is not None and boolean:
isMax=win.isMaximized()
w=win.widget()
#w.setParent(None)
sip.delete(w)#
#del w
win.setWidget(pw)
else:
self.view.addMdiSubWindow(MSView(pw), title, isMax)
self.view.mdiArea.tileSubWindows()
def startTask(self):
"""
Main Function (model function) Clustering
"""
MSDialogController.startTask(self)
#qApp.instance().view.showInStatusBar("Clustering Step...Please Wait..", 5000)
self.task = MSClusterThread(self.sampleList, **self.parameters)
QObject.connect(self.view, SIGNAL('destroyed(QObject *)'), self.task.begin)
#self.connect(self.view, SIGNAL('destroyed(QObject *)'), self.setViewToNone)
QObject.connect(self.task, SIGNAL("started()"),qApp.instance().view.to_determined_mode)
QObject.connect(self.task, SIGNAL('update_pb'), qApp.instance().view.updateProgressBar)
#QObject.connect(self.task, SIGNAL("finished()"),qApp.instance().view.to_determined_mode)
QObject.connect(self.task, SIGNAL("finished()"), self.setModels)
#print "about to close"
self.view.close()
def plotPeakSelection(self, index, boolean=False):
"""
Allow to plot peak and peak tables
"""
if not index.isValid():
return
data = index.data().toString().split("/")
prec, rt =float(data[0]), float(data[1])
peaks=self.getElementsToPlot(flags='peak', prec=prec, rt=rt)
pw = MSQtCanvas(peaks, "peak@%s/%s"%(str(prec), str(rt)),
labels={'bottom':'RT(s)', 'left':'INTENSITY'},
flags='peak')
QObject.connect(qApp.instance(), SIGNAL('redraw()'), pw.redraw)
title="peak@%s/%s"%(str(prec), str(rt))
win=self.view.mdiArea.activeSubWindow()
isMax=False
if win is not None and boolean:
isMax=win.isMaximized()
w=win.widget()
#w.connect(w, SIGNAL('destroyed (QObject *)'), self.destroyed)
#w.setParent(None)
sip.delete(w)
del w
win.setWidget(MSView(pw))
#win.close()
else:
self.view.addMdiSubWindow(MSView(pw), title, isMax)
self.view.mdiArea.tileSubWindows()
def plotSelection(self, index, boolean=False):
"""
Allow to plot spectrum
"""
if not index.isValid():
return
chromas=self.getElementsToPlot(flags='spectra', index=index.row())
title="Spectrum@%s"%str(chromas[0].rtmin)
legend={'bottom':'m/z', 'left':'INTENSITY'}
flags='spectra'
#useOpenGL=False
pw = MSQtCanvas(chromas, title, labels=legend, flags=flags)#, useOpenGL=useOpenGL)
QObject.connect(qApp.instance(), SIGNAL('redraw()'), pw.redraw)
a=self.view.mdiArea.activeSubWindow()
isMax=False
if a is not None and boolean:
isMax=a.isMaximized()
w=a.widget()
#w.connect(w, SIGNAL('destroyed (QObject *)'), self.destroyed)
#w.setParent(None)
#print "parent of w just before elimination", w.parent()
sip.delete(w)#; del w
del w
a.setWidget(pw)
#a.close()
else:
self.view.addMdiSubWindow(pw, title, isMax)
self.view.mdiArea.tileSubWindows()
def _workingOn(self):
# if self.acTree not in self.workingTrees: #can work by name too
# qApp.instance().view.showErrorMessage("Error", """<br>Error when trying to select items from treeView</br>
# #<p>Select a tab corresponding to the action you want""")
try:
self.view.lineEdit.setText(self.stringFormatting([spl.xmlfile for spl in qApp.instance().model if spl.checked]))
except AttributeError:
pass
def __init__(self, data, title, flags="chroma", parent=None, **k):
QWidget.__init__(self, parent)
MSDialogController.__init__(self, 0, parent)
self.model = self.qApp.model
self.view = self.qApp.view
self.data = data
self.title = title
self.flags = flags
if self.flags == 'peak':
if self.acTree not in (self.view.treeView_2, self.view.treeView_3):
print "Unknown Error"
return
idx = self.acTree.selectedIndexes()[0]
s = qApp.instance().dockControl.currentSample[
1 if self.acTree is self.view.treeView_2 else 2]
if s is None:
print "unknow error"
return
values = map(float, idx.data().toString().split('/')[:2])
self.currentPeak = s.peakAt(*values)
#connection to update the selected Peak object
self.connect(self.acTree, SIGNAL("changedLine"),
self.updateCurrentPeak)
self.minX, self.maxX, self.maxY = [0] * 3
#if flags != 'peak':
# self.minX, self.maxX, self.maxY = self.getMax()
self.pw = PlotWidget(self.minX, self.maxX, self.maxY, parent=self,
**k) #parent=self,
#self.pw.setAttribute(Qt.WA_DeleteOnClose)#plotItem.setAttribute(Qt.WA_PaintOnScreen & Qt.WA_PaintUnclipped)
if k.get('antialiased', False):
self.pw.setRenderHint(0x01) #antialiasing i suppose
self.pw.setTitle(title)
self.pw.updateGrid()
self._setupUi()
self.connect(self, SIGNAL('linePlotted'), self.updateContextMenu)
self.connect(self.view.sampleTableView,
SIGNAL("disHighlightRequested(QModelIndex)"),
self.disHighlightOne)
self.connect(self.view.sampleTableView,
SIGNAL("highlightRequested(QModelIndex)"), self.highlight)
self.connect(self.view.sampleTableView,
SIGNAL("noHighlightRequested()"), self.disHighlight)
self.connect(self.view.ppmEditer, SIGNAL('valueChanged(double)'),
self.redrawAll)
self.drawnItems = {}
self.trashItems = [] #why unecessary? nope to collect annotation stuff
self.textLabels = []
self.pixmaps = []
self.dataPoints = None
self._plotting(self.data) #initial plotting
def normalizeSamples(self):
if not self.model:
self.view.showErrorMessage("Error", "no sample found...")
return
class Dialog(QtGui.QDialog):
def __init__(self, parent=None):
QtGui.QDialog.__init__(self, parent)
self.setupUi()
self.connect(self.comboBox, SIGNAL('currentIndexChanged(const QString &)'), self.updateCombo)
self.connect(self.comboBox_2, SIGNAL('currentIndexChanged(const QString &)'), self.updateLabel)
self.peak = None
def setupUi(self):
v = QtGui.QVBoxLayout()
f = QtGui.QFormLayout()
self.comboBox = QtGui.QComboBox()
self.items = [spl.shortName() for spl in QApplication.instance().model]
self.comboBox.addItems(self.items)
f.addRow("Choose One sample", self.comboBox)
self.comboBox_2 = QtGui.QComboBox()
f.addRow("Peak", self.comboBox_2)
self.label = QtGui.QLabel()
f.addRow("Area", self.label)
self.checkBox = QtGui.QCheckBox("Apply to all", self)
self.buttonBox = QtGui.QDialogButtonBox(self)
self.buttonBox.setStandardButtons(QtGui.QDialogButtonBox.Ok | QtGui.QDialogButtonBox.Cancel)
v.addLayout(f)
v.addWidget(self.checkBox)
v.addWidget(self.buttonBox)
self.setLayout(v)
def updateCombo(self, string):
items = [str(p) for p in QApplication.instance().model.sample(string, fullNameEntry=False).irawPeaks()]
self.comboBox_2.clear()
self.comboBox_2.addItems(items)
def updateLabel(self, string):
self.peak = QApplication.instance().model.sample(self.comboBox.currentText(),
fullNameEntry=False).peakAt(*map(float, string.split('/')))
self.label.setText(str(self.peak.area))
dialog = Dialog(self.view)
dialog.setAttribute(QtCore.Qt.WA_DeleteOnClose)
dialog.updateCombo(qApp.instance().model[0].shortName())
def norm():
applyToAll = dialog.checkBox.isChecked()
samplesToTreat = [spl for spl in self.model] if applyToAll else [self.model.sample(dialog.comboBox.currentText(),
fullNameEntry=False)]
peak = dialog.peak
if peak is None:
return
dialog.close()
for spl in samplesToTreat:
spl.normalize(peak)
QObject.connect(dialog.buttonBox, SIGNAL('rejected()'), dialog.close)
QObject.connect(dialog.buttonBox, SIGNAL('accepted()'), norm)
dialog.exec_()
def startTask(self):
"""
Main Function (model function) Clustering
"""
MSDialogController.startTask(self)
#qApp.instance().view.showInStatusBar("Clustering Step...Please Wait..", 5000)
self.task = MSClusterThread(self.sampleList, **self.parameters)
QObject.connect(self.view, SIGNAL('destroyed(QObject *)'),
self.task.begin)
#self.connect(self.view, SIGNAL('destroyed(QObject *)'), self.setViewToNone)
QObject.connect(self.task, SIGNAL("started()"),
qApp.instance().view.to_determined_mode)
QObject.connect(self.task, SIGNAL('update_pb'),
qApp.instance().view.updateProgressBar)
#QObject.connect(self.task, SIGNAL("finished()"),qApp.instance().view.to_determined_mode)
QObject.connect(self.task, SIGNAL("finished()"), self.setModels)
#print "about to close"
self.view.close()
def _initialize(self):
"""
called in __init__ of msdialogcontroller
"""
settings = QSettings(
'INRA/INSA', '-'.join([
qApp.instance().APPLICATION_NAME_STR,
qApp.instance().VERSION_STR
]))
if isinstance(self.view, MSMatchedFilteredDialog):
settings.beginGroup("matchedFilteredDialog")
self.view.lineEdit_2.setText(
settings.value("lineEdit_2", "30").toString())
self.view.lineEdit_4.setText(
settings.value("lineEdit_4", "2").toString())
self.view.lineEdit_5.setText(
settings.value("lineEdit_5", "0.5").toString())
self.view.lineEdit_6.setText(
settings.value("lineEdit_6", "3").toString())
self.view.lineEdit_3.setText(
settings.value("lineEdit_3", "0.1").toString())
self.view.spinBox.setValue(settings.value("spinBox", 5).toInt()[0])
settings.endGroup()
elif isinstance(self.view, MSCentWaveDialog):
self.view.lineEdit_2.setText("300-3200")
self.view.lineEdit_4.setText("10-22")
self.view.lineEdit_5.setText("1000")
self.view.lineEdit_6.setText("1.2")
self.view.spinBox.setValue(10)
self.view.spinBox_2.setValue(10)
self.view.checkBox.setChecked(True)
self.view.lineEdit_7.setText("0.8")
self.view.lineEdit_8.setText("5")
self.view.lineEdit_9.setText("20")
self.view.lineEdit_10.setText("0.002")
self.view.obiwarp.setChecked(True)
self.view.gb_2.setChecked(False)
self.view.gb_3.setChecked(False)
def _workingOn(self):
# if self.acTree not in self.workingTrees: #can work by name too
# qApp.instance().view.showErrorMessage("Error", """<br>Error when trying to select items from treeView</br>
# #<p>Select a tab corresponding to the action you want""")
try:
self.view.lineEdit.setText(
self.stringFormatting([
spl.xmlfile for spl in qApp.instance().model if spl.checked
]))
except AttributeError:
pass
def startTask(self):
MSDialogController.startTask(self)
self.task = MSIntegrationThread(self.sampleList, **self.parameters)
def begin():
self.view = None
self.task.start()
self.task.exec_()
self.task.begin = begin
#to avoid QObject::killTimers error, wait for the dialog to be deleted
QObject.connect(self.view, SIGNAL('destroyed(QObject *)'),
self.task.begin)
QObject.connect(self.task, SIGNAL("started()"),
qApp.instance().view.to_indetermined_mode)
QObject.connect(self.task, SIGNAL("finished()"), self.setModels)
QObject.connect(self.task, SIGNAL("finished()"),
qApp.instance().view.to_determined_mode)
self.view.close()
def cleaningRepository(self, c):
in_, out, err =c.exec_command('cd work/ && ls')
res = qApp.instance().view.showWarningMessage("Non Empty remote repository",
"the remote repository is not empty, do you want to remove all files?")
if res!=4194304:
#c.exec_command('cd work/ && rm -rf *')#to much agressive
try:
c.exec_command('cd work && rm %s && rm %s'%(self.XCMS_SCRIPT, self.SHELL_SCRIPT))
except Exception:
pass
return True
return False
def startConnection(self):
"""
connection to remote server
can launch a thread checking every minute your mailbox...
"""
#if not self.directory:return
#self.parent().close()
self.close()
client = SSHClient()
client.set_missing_host_key_policy(AutoAddPolicy())
try:
client.connect(str(self.host.text()), username=str(self.username.text()), password=str(self.password.text()))
except SSHException: qApp.instance().showErrorMessage("Error", "The ssh session could not be established")
except AuthenticationException: qApp.instance().showErrorMessage("Error","Authentication failed")
except BadHostKeyException: qApp.instance().showErrorMessage("Error", "the server's host key could not be verified")
sftpCp = self.cleaningRepository(client)
if sftpCp:
sftp = client.open_sftp()
self.sftpCopying(sftp)
sftp.close()
else:
self.retrieveDirTree(c, out)
self.makeRScript(client)
self.makeShellScript(client)
if self.interactiveSession.isChecked():
import interactive
print ('invoking a shell')
chan = client.invoke_shell()
chan.send('bash\n')
interactive.interactive_shell(chan)
chan.close()
else:
self.launchCommand(client)
client.close()
def annotate(self):
text, bool_ = QInputDialog.getText(self.view, "Annotation dialog", "Annotation:")
g=QGraphicsTextItem(str(text))
g.setFlag(QGraphicsItem.ItemIgnoresTransformations)
g.setFlag(QGraphicsItem.ItemIsMovable)
g.setTextInteractionFlags(Qt.TextEditorInteraction)
font=qApp.instance().font()
font.setPointSizeF(10.)
g.setFont(font)
g.setDefaultTextColor(Qt.blue)
g.setPos(500,1e4)
self.trashItems.append(g)
self.pw.addItem(g)
def __init__(self, data, title, flags="chroma", parent=None, **k):
QWidget.__init__(self, parent)
MSDialogController.__init__(self, 0, parent)
self.model = self.qApp.model
self.view = self.qApp.view
self.data=data
self.title=title
self.flags=flags
if self.flags == 'peak':
if self.acTree not in (self.view.treeView_2, self.view.treeView_3):
print "Unknown Error"
return
idx=self.acTree.selectedIndexes()[0]
s = qApp.instance().dockControl.currentSample[1 if self.acTree is self.view.treeView_2 else 2]
if s is None:
print "unknow error"
return
values = map(float, idx.data().toString().split('/')[:2])
self.currentPeak = s.peakAt(*values)
#connection to update the selected Peak object
self.connect(self.acTree, SIGNAL("changedLine"), self.updateCurrentPeak)
self.minX, self.maxX, self.maxY = [0] * 3
#if flags != 'peak':
# self.minX, self.maxX, self.maxY = self.getMax()
self.pw = PlotWidget(self.minX, self.maxX, self.maxY, parent=self, **k)#parent=self,
#self.pw.setAttribute(Qt.WA_DeleteOnClose)#plotItem.setAttribute(Qt.WA_PaintOnScreen & Qt.WA_PaintUnclipped)
if k.get('antialiased', False):
self.pw.setRenderHint(0x01)#antialiasing i suppose
self.pw.setTitle(title)
self.pw.updateGrid()
self._setupUi()
self.connect(self, SIGNAL('linePlotted'), self.updateContextMenu)
self.connect(self.view.sampleTableView, SIGNAL("disHighlightRequested(QModelIndex)"), self.disHighlightOne)
self.connect(self.view.sampleTableView, SIGNAL("highlightRequested(QModelIndex)"), self.highlight)
self.connect(self.view.sampleTableView, SIGNAL("noHighlightRequested()"), self.disHighlight)
self.connect(self.view.ppmEditer, SIGNAL('valueChanged(double)'), self.redrawAll)
self.drawnItems = {}
self.trashItems=[]#why unecessary? nope to collect annotation stuff
self.textLabels = []
self.pixmaps = []
self.dataPoints = None
self._plotting(self.data)#initial plotting
def setModels(self):
"""
end processing
"""
qApp.instance().view.comparativeTableView.setModel(MSDialogController.actualizePeakModelComparative())
qApp.instance().view.showInformationMessage("Integration Done", "Integration process finished...")
qApp.instance().view.tabWidget.setCurrentIndex(1)
def activeTree(self, integer):
window = qApp.instance().view
if integer not in (0, 1, 2):
#raise ValueError("TreeView numeroted from 0 to 2")
return #no raising an error....
if integer == 0:
self.acTree = window.treeView
self.acModel = window.spectraModel
elif integer == 1:
self.acTree = window.treeView_2
self.acModel = window.peakModel
elif integer == 2:
self.acTree = window.treeView_3
self.acModel = window.clusterModel
def activeTree(self, integer):
window = qApp.instance().view
if integer not in (0, 1, 2):
#raise ValueError("TreeView numeroted from 0 to 2")
return #no raising an error....
if integer == 0:
self.acTree = window.treeView
self.acModel = window.spectraModel
elif integer == 1:
self.acTree = window.treeView_2
self.acModel = window.peakModel
elif integer == 2:
self.acTree = window.treeView_3
self.acModel = window.clusterModel
def annotate(self):
text, bool_ = QInputDialog.getText(self.view, "Annotation dialog",
"Annotation:")
g = QGraphicsTextItem(str(text))
g.setFlag(QGraphicsItem.ItemIgnoresTransformations)
g.setFlag(QGraphicsItem.ItemIsMovable)
g.setTextInteractionFlags(Qt.TextEditorInteraction)
font = qApp.instance().font()
font.setPointSizeF(10.)
g.setFont(font)
g.setDefaultTextColor(Qt.blue)
g.setPos(500, 1e4)
self.trashItems.append(g)
self.pw.addItem(g)
def cleaningRepository(self, c):
in_, out, err = c.exec_command('cd work/ && ls')
res = qApp.instance().view.showWarningMessage(
"Non Empty remote repository",
"the remote repository is not empty, do you want to remove all files?"
)
if res != 4194304:
#c.exec_command('cd work/ && rm -rf *')#to much agressive
try:
c.exec_command('cd work && rm %s && rm %s' %
(self.XCMS_SCRIPT, self.SHELL_SCRIPT))
except Exception:
pass
return True
return False
def setModels(self):
"""
end processing
"""
qApp.instance().view.comparativeTableView.setModel(
MSDialogController.actualizePeakModelComparative())
qApp.instance().view.showInformationMessage(
"Integration Done", "Integration process finished...")
qApp.instance().view.tabWidget.setCurrentIndex(1)
def getSftp(self):
client = SSHClient()
client.set_missing_host_key_policy(AutoAddPolicy())
try:
client.connect(str(self.host.text()), username=str(self.username.text()), password=str(self.password.text()))
except SSHException: qApp.instance().showErrorMessage("Error", "The ssh session could not be established")
except AuthenticationException: qApp.instance().showErrorMessage("Error","Authentication failed")
except BadHostKeyException: qApp.instance().showErrorMessage("Error", "the server's host key could not be verified")
sftp = client.open_sftp()
sftp.get('/work/matrice', './matrice')
sftp.close()
client.close()
def plotTICS(self):
chromas=self.getElementsToPlot(flags='chroma')
title="TICS"
legend={'bottom':'RT(s)', 'left':'INTENSITY'}
flags='chroma'
pw = MSQtCanvas(chromas, title, labels=legend, flags=flags)#, useOpenGL=useOpenGL)
QObject.connect(qApp.instance(), SIGNAL('redraw()'), pw.redraw)
a=self.view.mdiArea.activeSubWindow()
isMax=False
if a is not None:
isMax=a.isMaximized()
w=a.widget()
w.setParent(None)
sip.delete(w)
a.setWidget(pw)
else:
self.view.addMdiSubWindow(MSView(pw), title, isMax)
self.view.mdiArea.tileSubWindows()
def __init__(self, model, view):
"""constructor
@parameter view: the view (dialog)
@parameter model: the model, data to manipulate, string,
file, sample, sampleList...
@parent: it is admitted the view is the parent of her
controller
"""
self.view = view
self.model = model
self.acModel = None
self.acTree = None
window = self.qApp.view #to avoid error when using a QDialogController
self.activeTree(window.tabWidget.currentIndex())
QObject.connect(window.tabWidget, SIGNAL('currentChanged(int)'), self.activeTree)
QObject.connect(qApp.instance(), SIGNAL('modelChanged'), self.setModel) #update model, used for loading a project
self._buildConnections()
def plotTICS(self):
chromas = self.getElementsToPlot(flags='chroma')
title = "TICS"
legend = {'bottom': 'RT(s)', 'left': 'INTENSITY'}
flags = 'chroma'
pw = MSQtCanvas(chromas, title, labels=legend,
flags=flags) #, useOpenGL=useOpenGL)
QObject.connect(qApp.instance(), SIGNAL('redraw()'), pw.redraw)
a = self.view.mdiArea.activeSubWindow()
isMax = False
if a is not None:
isMax = a.isMaximized()
w = a.widget()
w.setParent(None)
sip.delete(w)
a.setWidget(pw)
else:
self.view.addMdiSubWindow(MSView(pw), title, isMax)
self.view.mdiArea.tileSubWindows()
def redo(self):
m = QApplication.instance().model
if self.rawData:
m.alignRawData(m)
else:
m.alignPeaksInRTDimension(m, self.polyDegree, self.errorRt)
for tree in (qApp.instance().view.treeView, qApp.instance().view.treeView_2, qApp.instance().view.treeView_3):
tree.removeAll()
for spl in qApp.instance().model:
MSDialogController.actualizeSpectraModel(spl)
if spl.rawPeaks:
MSDialogController.actualizePeakModel(spl)
if spl.mappedPeaks:
MSDialogController.actualizeClusterModel(spl)
qApp.instance().view.showInformationMessage('Alignment calculation done', "Alignment done")
def __init__(self, model, view):
"""constructor
@parameter view: the view (dialog)
@parameter model: the model, data to manipulate, string,
file, sample, sampleList...
@parent: it is admitted the view is the parent of her
controller
"""
self.view = view
self.model = model
self.acModel = None
self.acTree = None
window = self.qApp.view #to avoid error when using a QDialogController
self.activeTree(window.tabWidget.currentIndex())
QObject.connect(window.tabWidget, SIGNAL('currentChanged(int)'),
self.activeTree)
QObject.connect(
qApp.instance(), SIGNAL('modelChanged'),
self.setModel) #update model, used for loading a project
self._buildConnections()
def plotClusterSelection(self, index, boolean=False):
"""
Allow to plot peak and cluster tables
"""
if not index.isValid():
return
string = str(index.data().toString(
)) #.model().data(index.parent(), Qt.DisplayRole).toString()
if string in ("fragments/adducts:", "isotopic cluster:"):
return
data = string.split('/')
#print data
prec = float(data[0])
rt = float(data[1])
#print prec, rt
peaks = self.getElementsToPlot(flags='peak', prec=prec, rt=rt)
pw = ClusterWidget(
peaks, self.view
) #MSQtCanvas(peaks, "peak@%s/%s"%(str(prec), str(rt)), labels={'bottom':'RT(s)', 'left':'INTENSITY'}, flags='peak')
QObject.connect(qApp.instance(), SIGNAL('redraw()'),
pw.widget.mainWidget.redraw)
title = "peak@%s/%s" % (str(prec), str(rt))
win = self.view.mdiArea.activeSubWindow()
isMax = False
if win is not None and boolean:
isMax = win.isMaximized()
w = win.widget()
#w.setParent(None)
sip.delete(w) #
#del w
win.setWidget(pw)
else:
self.view.addMdiSubWindow(MSView(pw), title, isMax)
self.view.mdiArea.tileSubWindows()
def getSftp(self):
client = SSHClient()
client.set_missing_host_key_policy(AutoAddPolicy())
try:
client.connect(str(self.host.text()),
username=str(self.username.text()),
password=str(self.password.text()))
except SSHException:
qApp.instance().showErrorMessage(
"Error", "The ssh session could not be established")
except AuthenticationException:
qApp.instance().showErrorMessage("Error", "Authentication failed")
except BadHostKeyException:
qApp.instance().showErrorMessage(
"Error", "the server's host key could not be verified")
sftp = client.open_sftp()
sftp.get('/work/matrice', './matrice')
sftp.close()
client.close()
def startConnection(self):
"""
connection to remote server
can launch a thread checking every minute your mailbox...
"""
#if not self.directory:return
#self.parent().close()
self.close()
client = SSHClient()
client.set_missing_host_key_policy(AutoAddPolicy())
try:
client.connect(str(self.host.text()),
username=str(self.username.text()),
password=str(self.password.text()))
except SSHException:
qApp.instance().showErrorMessage(
"Error", "The ssh session could not be established")
except AuthenticationException:
qApp.instance().showErrorMessage("Error", "Authentication failed")
except BadHostKeyException:
qApp.instance().showErrorMessage(
"Error", "the server's host key could not be verified")
sftpCp = self.cleaningRepository(client)
if sftpCp:
sftp = client.open_sftp()
self.sftpCopying(sftp)
sftp.close()
else:
self.retrieveDirTree(c, out)
self.makeRScript(client)
self.makeShellScript(client)
if self.interactiveSession.isChecked():
import interactive
print('invoking a shell')
chan = client.invoke_shell()
chan.send('bash\n')
interactive.interactive_shell(chan)
chan.close()
else:
self.launchCommand(client)
client.close()
def stopped(self):
qApp.instance().win.actionStart.setChecked(False)
qApp.instance().win.statusbar.showMessage('Scada detenido')
def setParams():
multiCore = d.multiCore.isChecked()
lowMemory = d.lowMemory.isChecked()
d.close()
qApp.instance().multiCore = multiCore
qApp.instance().lowMemory = lowMemory
def _buildConnections(self):
#undo redo stuffs
QObject.connect(qApp.instance().undoStack,
SIGNAL('canRedoChanged(bool)'),
self.view.editMenu.actions()[1].setEnabled)
QObject.connect(qApp.instance().undoStack,
SIGNAL('canUndoChanged(bool)'),
self.view.editMenu.actions()[0].setEnabled)
#tooltip emulation TODO
QObject.connect(self.view.peakPickingMenu,
SIGNAL("hovered(QAction *)"),
self.view._actionHovered)
QObject.connect(self.view.fileMenu,
SIGNAL("hovered(QAction *)"),
self.view._actionHovered)
#file menu
QObject.connect(self.view.op.actions()[0],
SIGNAL("triggered()"),
self.openFile)
QObject.connect(self.view.op.actions()[1],
SIGNAL('triggered()'),
self.loadProject)
QObject.connect(self.view.fileMenu.actions()[1],
SIGNAL("triggered()"),
self.saveProject)
QObject.connect(self.view.fileMenu.actions()[2],
SIGNAL("triggered()"),
self.loadPeakList)
QObject.connect(self.view.fileMenu.actions()[3],
SIGNAL("triggered()"),
self.convertParameters)
QObject.connect(self.view.fileMenu.actions()[4],
SIGNAL("triggered()"),
self.launchBatch)
QObject.connect(self.view.fileMenu.actions()[5],
SIGNAL("triggered()"),
self.mergeFile)
QObject.connect(self.view.fileMenu.actions()[7],
SIGNAL("triggered()"),
self.quit)
#edit menu
QObject.connect(self.view.editMenu.actions()[0],
SIGNAL('triggered()'),
QApplication.instance().undoStack.undo)
QObject.connect(self.view.editMenu.actions()[1],
SIGNAL('triggered()'),
QApplication.instance().undoStack.redo)
QObject.connect(self.view.editMenu.actions()[3],
SIGNAL('triggered()'),
self.showSettings)
QObject.connect(self.view.exportMenu.actions()[0],
SIGNAL('triggered()'),
self.exportPeakList)
QObject.connect(self.view.exportMenu.actions()[1],
SIGNAL('triggered()'),
self.exportClusterMatrix)
#algo menu
QObject.connect(self.view.preProcessing.actions()[0],
SIGNAL('triggered()'),
self.smoothAllRawData)
QObject.connect(self.view.preProcessing.actions()[1],
SIGNAL('triggered()'),
self.baselineCorrection)
QObject.connect(self.view.preProcessing.actions()[2],
SIGNAL('triggered()'),
self.calibrate)
QObject.connect(self.view.preProcessing.actions()[3],
SIGNAL('triggered()'),
self.resizeSample)
QObject.connect(self.view.peakPickingMenu.actions()[0],
SIGNAL("triggered()"),
self.integrationParameters)
QObject.connect(self.view.peakPickingMenu.actions()[1],
SIGNAL("triggered()"),
self.centWaveParameters)
#alignment
QObject.connect(self.view.alignment.actions()[0],
SIGNAL("triggered()"),
self.alignmentByPolyFit)
QObject.connect(self.view.alignment.actions()[1],
SIGNAL('triggered()'),
self.alignmentByDtw)
QObject.connect(self.view.alignment.actions()[2],
SIGNAL("triggered()"),
self.alignmentByObiWarp)
QObject.connect(self.view.algoMenu.actions()[3],
SIGNAL('triggered()'),
self.normalizeSamples)
QObject.connect(self.view.algoMenu.actions()[4],
SIGNAL("triggered()"),
self.clusteringParameters)
QObject.connect(self.view.algoMenu.actions()[5],
SIGNAL("triggered()"),
self.identificationParameters)
#view menu
QObject.connect(self.view.plotting.actions()[0],
SIGNAL("triggered()"),
self.show3DView)
#QObject.connect(self.view.plotting.actions()[1],
# SIGNAL("triggered()"),
# self.launchCytoscape)
QObject.connect(self.view.plotting.actions()[1],
SIGNAL("triggered()"),
self.showSpectrogramView)
#self.connect(self.view.plotting.actions()[3],
# SIGNAL("triggered()"),
# self.showAlignedData)
#tools menu
QObject.connect(self.view.toolsMenu.actions()[0],
SIGNAL("triggered()"),
self.launchWebNavigator)
#QObject.connect(self.view.toolsMenu.actions()[1],
# SIGNAL("triggered()"),
# self.launchCytoscape)
QObject.connect(self.view.toolsMenu.actions()[1],
SIGNAL("triggered()"),
self.launchEricEditor)
QObject.connect(self.view.toolsMenu.actions()[2],
SIGNAL("triggered()"),
self.showPeriodicTable)
#plugins menu
QObject.connect(self.view.launchingMenu,
SIGNAL('triggered(QAction*)'),
self.loadPlugin)
QObject.connect(self.view.pluginMenu.actions()[2],
SIGNAL('triggered()'),
self.deletePlugs)
#about
QObject.connect(self.view.aboutMenu.actions()[0],
SIGNAL("triggered()"),
self.view.showMetMSInformation)
QObject.connect(self.view.aboutMenu.actions()[1],
SIGNAL("triggered()"),
self.showQtInformation)
QObject.connect(self.view.aboutMenu.actions()[2],
SIGNAL("triggered()"),
self.showDocumentation)
def packageRecieved(self, pkg):
PicnetSCADAProtocol.packageRecieved(self, pkg)
cadena = "%s\n" % pkg.hex_dump()
qApp.instance().emit(SIGNAL('data_received'), cadena)
def undo(self):
qApp.instance().model=self.model
qApp.instance().currentModelChanged()
qApp.instance().view.spectraModel = self.spectraModel
qApp.instance().view.peakModel = self.peakModel
qApp.instance().view.clusterModel = self.clusterModel
qApp.instance().view.treeView.setModel(qApp.instance().view.spectraModel)
qApp.instance().view.treeView_2.setModel(qApp.instance().view.peakModel)
qApp.instance().view.treeView_3.setModel(qApp.instance().view.clusterModel)
qApp.instance().view.showInformationMessage('Alignment Undone', 'Alignment Undone')
def _plotting(self, data):
"""
refactor this shit
c = Line(chrom.x_data, chrom.y_data,
QColor.fromRgbF(*(self.ref.sample.color+(.7,))),
parent=self.pw.plotItem.vb,
scene=self.pw.scene())
#test scatter plot
self.scatter = ScatterPlotItem(x=chrom.x_data, y=chrom.y_data)
self.pw.addDataItem(self.scatter)
self.scatter.sigClicked.connect(self.requestSpectra)
"""
if self.flags == 'peak':
self.connect(self.pw.plotItem.vb,
SIGNAL('showDiffOrSpectra(PyQt_PyObject)'),
self.drawSpectra)
self.ref = sorted([e for e in data if e is not None],
key=lambda x: x.height)[-1]
ppm = self.view.ppmEditer.value() if self.view.usePpm.isChecked(
) else self.ref.sample.ppm
chrom = self.ref.sample.massExtraction(self.ref.mass(),
ppm,
asChromatogram=True)
#show labels
self.textLabels += self.showTextLabel(chrom.x_data, chrom.y_data)
#drawing
color = QColor.fromRgbF(*self.ref.sample.color + (.5, ))
c = self.pw.plotItem.plot(chrom.x_data, chrom.y_data, pen=color)
self.drawnItems[self.ref.sample] = c
# peak's pixmap on the ref peak
pix = PeakArrowItem(self.ref,
pen=color,
brush=color,
pos=(self.ref.rt, self.ref.height +
(self.ref.height * 6) / 100.),
angle=-90,
parent=self.pw.plotItem.vb)
pix.setZValue(1000)
self.pw.addItem(pix)
#both these connections are emitted
#in peak Indicator by effictivamente qApp
self.connect(qApp.instance(), SIGNAL("highlightRequested"),
c.setHighlighted)
self.connect(qApp.instance(), SIGNAL('updateBarPlot'),
self.barPlot.setPeakGroup) #
self.emit(SIGNAL('linePlotted'), self.ref.sample.shortName())
#if qApp.instance().lowMemory:
# chromatograms=[el.sample.loadAndExtract(el.mass(), el.sample.ppm, asChromatogram=True) \
# for el in data if el != ref and el is not None]
#else:
ppm = self.view.ppmEditer.value() if self.view.usePpm.isChecked(
) else self.ref.sample.ppm
chromatograms=[el.sample.massExtraction(el.mass(), ppm, asChromatogram=True) \
for el in data if el is not None and el != self.ref]
self.drawEics(chromatograms)
#initialisation zoom on the peak
self.pw.setYRange(0.,
self.ref.height + (self.ref.height * 12) / 100.)
self.pw.setXRange(self.ref.rtmin - 20, self.ref.rtmax + 20)
elif self.flags == 'chroma':
ref = [d for d in data if d is not None]
if not ref:
print "Error, empty data to plot"
return
self.ref = ref[0]
self.textLabels += self.showTextLabel(self.ref.x_data,
self.ref.y_data)
self.drawEics(data)
else: #spectrum
if not data:
#print "NOTHING TO PLOT"
return
self.ref = data[0]
for el in data:
c = SpectrumItem(el, centroid=True, scene=self.pw.scene())
self.pw.addItem(c)
self.drawnItems[el.sample] = c
self.pw.plotItem.curves.append(c)
self.emit(SIGNAL('linePlotted'), el.sample.shortName())
#just put time information
if data:
i = 0
while data[i] is None and i < len(data):
i += 1
self.textLabels += self.showTextLabel(data[i].x_data,
data[i].y_data)
#setting the range
#warning: autoRange pw function does not work well
#on spectrum item
maxY = max([el.y_data.max() for el in data])
minX, maxX = min([el.x_data.min() for el in data
]), max([el.x_data.max() for el in data])
self.pw.setXRange(minX, maxX, padding=0)
self.pw.setYRange(0., maxY, padding=0)
def started(self):
qApp.instance().win.statusbar.showMessage('Scada iniciado')
