def setupPlottingWidgets(self):
self.plotconfigs = (None, dict(shade=0.35, linewidth=1, color="g"))
self.rtPlotter = RtPlotter(rangeSelectionCallback=self.plotMz)
self.rtPlotter.setMinimumSize(300, 100)
self.mzPlotter = MzPlotter()
self.mzPlotter.setMinimumSize(300, 100)
pol = QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)
pol.setVerticalStretch(5)
self.rtPlotter.widget.setSizePolicy(pol)
self.mzPlotter.widget.setSizePolicy(pol)
def setupPlottingWidgets(self):
self.plotconfigs = (None, dict(shade=0.35, linewidth=1, color="g") )
self.rtPlotter = RtPlotter(rangeSelectionCallback=self.plotMz)
self.rtPlotter.setMinimumSize(300, 100)
self.mzPlotter = MzPlotter()
self.mzPlotter.setMinimumSize(300, 100)
pol = QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)
pol.setVerticalStretch(5)
self.rtPlotter.widget.setSizePolicy(pol)
self.mzPlotter.widget.setSizePolicy(pol)
class TableExplorer(QDialog):
def __init__(self, tables, offerAbortOption):
QDialog.__init__(self)
# Destroying the C++ object right after closing the dialog box,
# otherwise it may be garbage-collected in another QThread
# (e.g. the editor's analysis thread in Spyder), thus leading to
# a segmentation fault on UNIX or an application crash on Windows
self.setAttribute(Qt.WA_DeleteOnClose)
self.setWindowFlags(Qt.Window)
self.offerAbortOption = offerAbortOption
self.models = [TableModel(table, self) for table in tables]
self.model = None
self.tableView = None
self.currentRowIdx = -1
self.hadFeatures = None
self.wasIntegrated = None
self.setupWidgets()
self.setupLayout()
self.connectSignals()
sizePolicy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.setSizePolicy(sizePolicy)
self.setSizeGripEnabled(True)
self.setupViewForTable(0)
def setupWidgets(self):
self.setupMenuBar()
self.setupTableViews()
self.setupPlottingWidgets()
self.chooseSpectrum = QComboBox()
self.setupIntegrationWidgets()
if self.offerAbortOption:
self.setupAcceptButtons()
def setupMenuBar(self):
self.menubar = QMenuBar(self)
menu = self.buildEditMenu()
self.menubar.addMenu(menu)
self.chooseTableActions = []
if len(self.models) > 1:
menu = self.buildChooseTableMenu()
self.menubar.addMenu(menu)
def buildEditMenu(self):
self.undoAction = QAction("Undo", self)
self.undoAction.setShortcut(QKeySequence("Ctrl+Z"))
self.redoAction = QAction("Redo", self)
self.redoAction.setShortcut(QKeySequence("Ctrl+Y"))
menu = QMenu("Edit", self.menubar)
menu.addAction(self.undoAction)
menu.addAction(self.redoAction)
return menu
def setupTableViews(self):
self.tableViews = []
for i, model in enumerate(self.models):
self.tableViews.append(self.setupTableViewFor(model))
def setupTableViewFor(self, model):
tableView = QTableView(self)
@protect_signal_handler
def handler(evt, view=tableView, model=model, self=self):
if not view.isSortingEnabled():
view.setSortingEnabled(True)
view.resizeColumnsToContents()
model.emptyActionStack()
self.updateMenubar()
tableView.showEvent = handler
tableView.setModel(model)
tableView.horizontalHeader().setResizeMode(QHeaderView.Interactive)
pol = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
tableView.setSizePolicy(pol)
tableView.setVisible(False)
# before filling the table, disabling sorting accelerates table
# construction, sorting is enabled in TableView.showEvent, which is
# called after construction
tableView.setSortingEnabled(False)
return tableView
def buildChooseTableMenu(self):
menu = QMenu("Choose Table", self.menubar)
for i, model in enumerate(self.models):
action = QAction(" [%d]: %s" % (i, model.getTitle()), self)
menu.addAction(action)
self.chooseTableActions.append(action)
return menu
def setupPlottingWidgets(self):
self.plotconfigs = (None, dict(shade=0.35, linewidth=1, color="g"))
self.rtPlotter = RtPlotter(rangeSelectionCallback=self.plotMz)
self.rtPlotter.setMinimumSize(300, 100)
self.mzPlotter = MzPlotter()
self.mzPlotter.setMinimumSize(300, 100)
pol = QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)
pol.setVerticalStretch(5)
self.rtPlotter.widget.setSizePolicy(pol)
self.mzPlotter.widget.setSizePolicy(pol)
def setupIntegrationWidgets(self):
self.intLabel = QLabel("Integration")
self.chooseIntMethod = QComboBox()
import configs
for name, _ in configs.peakIntegrators:
self.chooseIntMethod.addItem(name)
self.choosePostfix = QComboBox()
self.reintegrateButton = QPushButton()
self.reintegrateButton.setText("Integrate")
def setupAcceptButtons(self):
self.okButton = QPushButton("Ok")
self.abortButton = QPushButton("Abort")
self.result = 1 # default for closing
def setupLayout(self):
vlayout = QVBoxLayout()
self.setLayout(vlayout)
vsplitter = QSplitter()
vsplitter.setOrientation(Qt.Vertical)
vsplitter.setOpaqueResize(False)
vsplitter.addWidget(self.menubar)
vsplitter.addWidget(self.layoutWidgetsAboveTable())
vsplitter.addWidget(self.chooseSpectrum)
for view in self.tableViews:
vsplitter.addWidget(view)
vlayout.addWidget(vsplitter)
if self.offerAbortOption:
vlayout.addLayout(self.layoutButtons())
def layoutButtons(self):
hbox = QHBoxLayout()
hbox.addWidget(self.abortButton)
hbox.setAlignment(self.abortButton, Qt.AlignVCenter)
hbox.addWidget(self.okButton)
hbox.setAlignment(self.okButton, Qt.AlignVCenter)
return hbox
def layoutWidgetsAboveTable(self):
hsplitter = QSplitter()
hsplitter.setOpaqueResize(False)
hsplitter.addWidget(self.rtPlotter.widget)
integrationLayout = QVBoxLayout()
integrationLayout.setSpacing(10)
integrationLayout.setMargin(5)
integrationLayout.addWidget(self.intLabel)
integrationLayout.addWidget(self.chooseIntMethod)
integrationLayout.addWidget(self.choosePostfix)
integrationLayout.addWidget(self.reintegrateButton)
integrationLayout.addStretch()
integrationLayout.setAlignment(self.intLabel, Qt.AlignTop)
integrationLayout.setAlignment(self.chooseIntMethod, Qt.AlignTop)
integrationLayout.setAlignment(self.reintegrateButton, Qt.AlignTop)
self.integrationFrame = QFrame()
self.integrationFrame.setLayout(integrationLayout)
hsplitter.addWidget(self.integrationFrame)
hsplitter.addWidget(self.mzPlotter.widget)
return hsplitter
def setupModelDependendLook(self):
hasFeatures = self.model.hasFeatures()
isIntegrated = self.model.isIntegrated()
self.hasFeatures = hasFeatures
self.isIntegrated = isIntegrated
self.setWindowTitle(self.model.getTitle())
self.chooseSpectrum.setVisible(False)
if hasFeatures != self.hadFeatures:
self.setPlotVisibility(hasFeatures)
self.hadFeatures = hasFeatures
# default: invisible, only activated when row clicked and
# level >= 2 spectra are available
if isIntegrated != self.wasIntegrated:
self.setIntegrationPanelVisiblity(isIntegrated)
self.wasIntegrated = isIntegrated
if hasFeatures:
self.rtPlotter.setEnabled(True)
self.resetPlots()
def setPlotVisibility(self, doShow):
self.rtPlotter.widget.setVisible(doShow)
self.mzPlotter.widget.setVisible(doShow)
def resetPlots(self):
self.rtPlotter.reset()
self.mzPlotter.reset()
def setIntegrationPanelVisiblity(self, doShow):
self.integrationFrame.setVisible(doShow)
@protect_signal_handler
def handleClick(self, index, model):
content = model.data(index)
if isUrl(content):
QDesktopServices.openUrl(QUrl(content))
def connectSignals(self):
for i, action in enumerate(self.chooseTableActions):
handler = lambda i=i: self.setupViewForTable(i)
handler = protect_signal_handler(handler)
self.menubar.connect(action, SIGNAL("triggered()"), handler)
for view in self.tableViews:
vh = view.verticalHeader()
vh.setContextMenuPolicy(Qt.CustomContextMenu)
self.connect(vh, SIGNAL("customContextMenuRequested(QPoint)"),\
self.openContextMenu)
self.connect(vh, SIGNAL("sectionClicked(int)"), self.rowClicked)
model = view.model()
handler = lambda idx, model=model: self.handleClick(idx, model)
handler = protect_signal_handler(handler)
self.connect(view, SIGNAL("clicked(QModelIndex)"), handler)
self.connect(self.reintegrateButton, SIGNAL("clicked()"),
self.doIntegrate)
self.connect(self.chooseSpectrum, SIGNAL("activated(int)"),
self.spectrumChosen)
if self.offerAbortOption:
self.connect(self.okButton, SIGNAL("clicked()"), self.ok)
self.connect(self.abortButton, SIGNAL("clicked()"), self.abort)
def disconnectModelSignals(self):
self.disconnect(
self.model,
SIGNAL("dataChanged(QModelIndex,QModelIndex,PyQt_PyObject)"),
self.dataChanged)
self.menubar.disconnect(self.undoAction, SIGNAL("triggered()"),\
protect_signal_handler(self.model.undoLastAction))
self.menubar.disconnect(self.redoAction, SIGNAL("triggered()"),\
protect_signal_handler(self.model.redoLastAction))
def connectModelSignals(self):
self.connect(
self.model,
SIGNAL("dataChanged(QModelIndex,QModelIndex,PyQt_PyObject)"),
self.dataChanged)
self.menubar.connect(self.undoAction, SIGNAL("triggered()"),\
protect_signal_handler(self.model.undoLastAction))
self.menubar.connect(self.redoAction, SIGNAL("triggered()"),\
protect_signal_handler(self.model.redoLastAction))
def updateMenubar(self):
undoInfo = self.model.infoLastAction()
redoInfo = self.model.infoRedoAction()
self.undoAction.setEnabled(undoInfo != None)
self.redoAction.setEnabled(redoInfo != None)
if undoInfo:
self.undoAction.setText("Undo: %s" % undoInfo)
if redoInfo:
self.redoAction.setText("Redo: %s" % redoInfo)
def setupViewForTable(self, i):
for j, action in enumerate(self.chooseTableActions):
txt = str(action.text()) # QString -> Python str
if txt.startswith("*"):
txt = " " + txt[1:]
action.setText(txt)
if i == j:
action.setText("*" + txt[1:])
for j in range(len(self.models)):
self.tableViews[j].setVisible(i == j)
if self.model is not None:
self.disconnectModelSignals()
self.model = self.models[i]
self.tableView = self.tableViews[i]
self.setupModelDependendLook()
if self.isIntegrated:
self.model.setNonEditable("method", ["area", "rmse", "method",\
"params"])
self.choosePostfix.clear()
mod = self.model
for p in mod.table.supportedPostfixes(mod.integrationColNames()):
self.choosePostfix.addItem(repr(p))
if len(self.choosePostfix) == 1:
self.choosePostfix.setVisible(False)
self.connectModelSignals()
self.updateMenubar()
@protect_signal_handler
def dataChanged(self, ix1, ix2, src):
minr, maxr = sorted((ix1.row(), ix2.row()))
minc, maxc = sorted((ix1.column(), ix2.column()))
for r in range(minr, maxr + 1):
for c in range(minc, maxc + 1):
idx = self.model.createIndex(r, c)
self.tableView.update(idx)
if self.hasFeatures:
minr, maxr = sorted((ix1.row(), ix2.row()))
if minr <= self.currentRowIdx <= maxr:
if isinstance(src, IntegrateAction):
self.updatePlots(reset=False)
else:
self.updatePlots(reset=True)
@protect_signal_handler
def abort(self):
self.result = 1
self.close()
@protect_signal_handler
def ok(self):
self.result = 0
self.close()
@protect_signal_handler
def openContextMenu(self, point):
idx = self.tableView.verticalHeader().logicalIndexAt(point)
menu = QMenu()
cloneAction = menu.addAction("Clone row")
removeAction = menu.addAction("Delete row")
undoInfo = self.model.infoLastAction()
redoInfo = self.model.infoRedoAction()
if undoInfo is not None:
undoAction = menu.addAction("Undo %s" % undoInfo)
if redoInfo is not None:
redoAction = menu.addAction("Redo %s" % redoInfo)
appearAt = self.tableView.verticalHeader().mapToGlobal(point)
choosenAction = menu.exec_(appearAt)
if choosenAction == removeAction:
self.model.removeRow(idx)
elif choosenAction == cloneAction:
self.model.cloneRow(idx)
elif undoInfo is not None and choosenAction == undoAction:
self.model.undoLastAction()
elif redoInfo is not None and choosenAction == redoAction:
self.model.redoLastAction()
@protect_signal_handler
def doIntegrate(self):
if self.currentRowIdx < 0:
return # no row selected
# QString -> Python str:
method = str(self.chooseIntMethod.currentText())
# Again QString -> Python str.
# For better readibilty we put single quotes around the postfix
# entry in the QComboBox which we have to remove now:
postfix = str(self.choosePostfix.currentText()).strip("'")
rtmin, rtmax = self.rtPlotter.getRangeSelectionLimits()
self.model.integrate(postfix, self.currentRowIdx, method, rtmin, rtmax)
@protect_signal_handler
def rowClicked(self, rowIdx):
if not self.hasFeatures:
return
self.currentRowIdx = rowIdx
self.rtPlotter.setEnabled(True)
self.updatePlots(reset=True)
if self.hasFeatures:
self.setupSpectrumChooser()
def setupSpectrumChooser(self):
# delete QComboBox:
while self.chooseSpectrum.count():
self.chooseSpectrum.removeItem(0)
# get current spectra
rowidx = self.currentRowIdx
postfixes, spectra = self.model.getLevelNSpectra(rowidx, minLevel=2)
self.currentLevelNSpecs = []
if not len(spectra):
self.chooseSpectrum.setVisible(False)
return
self.chooseSpectrum.setVisible(True)
self.chooseSpectrum.addItem("Show only Level 1 spectra")
for postfix, s in zip(postfixes, spectra):
if postfix != "":
txt = postfix + ", "
else:
txt = ""
txt += "rt=%.2fm, level=%d" % (s.rt / 60.0, s.msLevel)
mzs = [mz for (mz, I) in s.precursors]
precursors = ", ".join("%.6f" % mz for mz in mzs)
if precursors:
txt += ", precursor mzs=[%s]" % precursors
self.chooseSpectrum.addItem(txt)
self.currentLevelNSpecs.append(s)
def updatePlots(self, reset=False):
rowIdx = self.currentRowIdx
eics, mzmin, mzmax, rtmin, rtmax, allrts = self.model.getEics(rowIdx)
curves = eics
configs = configsForEics(eics)
if self.isIntegrated:
smootheds = self.model.getSmoothedEics(rowIdx, allrts)
if smootheds is not None:
curves += smootheds
configs += configsForSmootheds(smootheds)
if not reset:
rtmin, rtmax = self.rtPlotter.getRangeSelectionLimits()
xmin, xmax, ymin, ymax = self.rtPlotter.getLimits()
self.rtPlotter.plot(curves,
configs=configs,
titles=None,
withmarker=True)
# allrts are sorted !
w = rtmax - rtmin
if w == 0:
w = 30.0 # seconds
self.rtPlotter.setRangeSelectionLimits(rtmin, rtmax)
self.rtPlotter.setXAxisLimits(rtmin - w, rtmax + w)
self.rtPlotter.replot()
if not reset:
self.rtPlotter.setXAxisLimits(xmin, xmax)
self.rtPlotter.setYAxisLimits(ymin, ymax)
self.rtPlotter.updateAxes()
reset = reset and mzmin is not None and mzmax is not None
limits = (mzmin, mzmax) if reset else None
self.plotMz(resetLimits=limits)
@protect_signal_handler
def spectrumChosen(self, idx):
if idx == 0:
self.rtPlotter.setEnabled(True)
self.chooseIntMethod.setEnabled(True)
self.reintegrateButton.setEnabled(True)
self.plotMz()
else:
self.rtPlotter.setEnabled(False)
self.chooseIntMethod.setEnabled(False)
self.reintegrateButton.setEnabled(False)
self.mzPlotter.plot([self.currentLevelNSpecs[idx - 1].peaks])
self.mzPlotter.resetAxes()
self.mzPlotter.replot()
def plotMz(self, resetLimits=None):
""" this one is used from updatePlots and the rangeselectors
callback """
rtmin = self.rtPlotter.minRTRangeSelected
rtmax = self.rtPlotter.maxRTRangeSelected
# get spectra for current row in given rt-range:
peakmaps = self.model.getPeakmaps(self.currentRowIdx)
peaks = [
pm.getDominatingPeakmap().ms1Peaks(rtmin, rtmax) for pm in peakmaps
]
# plot peaks
configs = configsForSpectra(peaks)
postfixes = self.model.table.supportedPostfixes(
self.model.eicColNames())
titles = map(repr, postfixes)
self.mzPlotter.plot(peaks, configs,
titles if len(titles) > 1 else None)
if resetLimits:
mzmin, mzmax = resetLimits
Imaxes = []
for p in peaks:
imin = p[:, 0].searchsorted(mzmin)
imax = p[:, 0].searchsorted(mzmax, side='right')
found = p[imin:imax, 1]
if len(found):
Imaxes.append(found.max())
if len(Imaxes) == 0:
Imax = 1.0
else:
Imax = max(Imaxes) * 1.2
self.mzPlotter.setXAxisLimits(mzmin, mzmax)
self.mzPlotter.reset_y_limits(0, Imax)
# plot() needs replot() afterwards !
self.mzPlotter.replot()
class TableExplorer(QDialog):
def __init__(self, tables, offerAbortOption):
QDialog.__init__(self)
# Destroying the C++ object right after closing the dialog box,
# otherwise it may be garbage-collected in another QThread
# (e.g. the editor's analysis thread in Spyder), thus leading to
# a segmentation fault on UNIX or an application crash on Windows
self.setAttribute(Qt.WA_DeleteOnClose)
self.setWindowFlags(Qt.Window)
self.offerAbortOption = offerAbortOption
self.models = [TableModel(table, self) for table in tables]
self.model = None
self.tableView = None
self.currentRowIdx = -1
self.hadFeatures = None
self.wasIntegrated = None
self.setupWidgets()
self.setupLayout()
self.connectSignals()
sizePolicy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.setSizePolicy(sizePolicy)
self.setSizeGripEnabled(True)
self.setupViewForTable(0)
def setupWidgets(self):
self.setupMenuBar()
self.setupTableViews()
self.setupPlottingWidgets()
self.chooseSpectrum = QComboBox()
self.setupIntegrationWidgets()
if self.offerAbortOption:
self.setupAcceptButtons()
def setupMenuBar(self):
self.menubar = QMenuBar(self)
menu = self.buildEditMenu()
self.menubar.addMenu(menu)
self.chooseTableActions = []
if len(self.models)>1:
menu = self.buildChooseTableMenu()
self.menubar.addMenu(menu)
def buildEditMenu(self):
self.undoAction = QAction("Undo", self)
self.undoAction.setShortcut(QKeySequence("Ctrl+Z"))
self.redoAction = QAction("Redo", self)
self.redoAction.setShortcut(QKeySequence("Ctrl+Y"))
menu = QMenu("Edit", self.menubar)
menu.addAction(self.undoAction)
menu.addAction(self.redoAction)
return menu
def setupTableViews(self):
self.tableViews = []
for i, model in enumerate(self.models):
self.tableViews.append(self.setupTableViewFor(model))
def setupTableViewFor(self, model):
tableView = QTableView(self)
@protect_signal_handler
def handler(evt, view=tableView, model=model, self=self):
if not view.isSortingEnabled():
view.setSortingEnabled(True)
view.resizeColumnsToContents()
model.emptyActionStack()
self.updateMenubar()
tableView.showEvent = handler
tableView.setModel(model)
tableView.horizontalHeader().setResizeMode(QHeaderView.Interactive)
pol = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
tableView.setSizePolicy(pol)
tableView.setVisible(False)
# before filling the table, disabling sorting accelerates table
# construction, sorting is enabled in TableView.showEvent, which is
# called after construction
tableView.setSortingEnabled(False)
return tableView
def buildChooseTableMenu(self):
menu = QMenu("Choose Table", self.menubar)
for i, model in enumerate(self.models):
action = QAction(" [%d]: %s" % (i,model.getTitle()), self)
menu.addAction(action)
self.chooseTableActions.append(action)
return menu
def setupPlottingWidgets(self):
self.plotconfigs = (None, dict(shade=0.35, linewidth=1, color="g") )
self.rtPlotter = RtPlotter(rangeSelectionCallback=self.plotMz)
self.rtPlotter.setMinimumSize(300, 100)
self.mzPlotter = MzPlotter()
self.mzPlotter.setMinimumSize(300, 100)
pol = QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)
pol.setVerticalStretch(5)
self.rtPlotter.widget.setSizePolicy(pol)
self.mzPlotter.widget.setSizePolicy(pol)
def setupIntegrationWidgets(self):
self.intLabel = QLabel("Integration")
self.chooseIntMethod = QComboBox()
import configs
for name, _ in configs.peakIntegrators:
self.chooseIntMethod.addItem(name)
self.choosePostfix = QComboBox()
self.reintegrateButton = QPushButton()
self.reintegrateButton.setText("Integrate")
def setupAcceptButtons(self):
self.okButton = QPushButton("Ok")
self.abortButton = QPushButton("Abort")
self.result = 1 # default for closing
def setupLayout(self):
vlayout = QVBoxLayout()
self.setLayout(vlayout)
vsplitter = QSplitter()
vsplitter.setOrientation(Qt.Vertical)
vsplitter.setOpaqueResize(False)
vsplitter.addWidget(self.menubar)
vsplitter.addWidget(self.layoutWidgetsAboveTable())
vsplitter.addWidget(self.chooseSpectrum)
for view in self.tableViews:
vsplitter.addWidget(view)
vlayout.addWidget(vsplitter)
if self.offerAbortOption:
vlayout.addLayout(self.layoutButtons())
def layoutButtons(self):
hbox = QHBoxLayout()
hbox.addWidget(self.abortButton)
hbox.setAlignment(self.abortButton, Qt.AlignVCenter)
hbox.addWidget(self.okButton)
hbox.setAlignment(self.okButton, Qt.AlignVCenter)
return hbox
def layoutWidgetsAboveTable(self):
hsplitter = QSplitter()
hsplitter.setOpaqueResize(False)
hsplitter.addWidget(self.rtPlotter.widget)
integrationLayout = QVBoxLayout()
integrationLayout.setSpacing(10)
integrationLayout.setMargin(5)
integrationLayout.addWidget(self.intLabel)
integrationLayout.addWidget(self.chooseIntMethod)
integrationLayout.addWidget(self.choosePostfix)
integrationLayout.addWidget(self.reintegrateButton)
integrationLayout.addStretch()
integrationLayout.setAlignment(self.intLabel, Qt.AlignTop)
integrationLayout.setAlignment(self.chooseIntMethod, Qt.AlignTop)
integrationLayout.setAlignment(self.reintegrateButton, Qt.AlignTop)
self.integrationFrame = QFrame()
self.integrationFrame.setLayout(integrationLayout)
hsplitter.addWidget(self.integrationFrame)
hsplitter.addWidget(self.mzPlotter.widget)
return hsplitter
def setupModelDependendLook(self):
hasFeatures = self.model.hasFeatures()
isIntegrated = self.model.isIntegrated()
self.hasFeatures = hasFeatures
self.isIntegrated = isIntegrated
self.setWindowTitle(self.model.getTitle())
self.chooseSpectrum.setVisible(False)
if hasFeatures != self.hadFeatures:
self.setPlotVisibility(hasFeatures)
self.hadFeatures = hasFeatures
# default: invisible, only activated when row clicked and
# level >= 2 spectra are available
if isIntegrated != self.wasIntegrated:
self.setIntegrationPanelVisiblity(isIntegrated)
self.wasIntegrated = isIntegrated
if hasFeatures:
self.rtPlotter.setEnabled(True)
self.resetPlots()
def setPlotVisibility(self, doShow):
self.rtPlotter.widget.setVisible(doShow)
self.mzPlotter.widget.setVisible(doShow)
def resetPlots(self):
self.rtPlotter.reset()
self.mzPlotter.reset()
def setIntegrationPanelVisiblity(self, doShow):
self.integrationFrame.setVisible(doShow)
@protect_signal_handler
def handleClick(self, index, model):
content = model.data(index)
if isUrl(content):
QDesktopServices.openUrl(QUrl(content))
def connectSignals(self):
for i, action in enumerate(self.chooseTableActions):
handler = lambda i=i: self.setupViewForTable(i)
handler = protect_signal_handler(handler)
self.menubar.connect(action, SIGNAL("triggered()"), handler)
for view in self.tableViews:
vh = view.verticalHeader()
vh.setContextMenuPolicy(Qt.CustomContextMenu)
self.connect(vh, SIGNAL("customContextMenuRequested(QPoint)"),\
self.openContextMenu)
self.connect(vh, SIGNAL("sectionClicked(int)"), self.rowClicked)
model = view.model()
handler = lambda idx, model=model: self.handleClick(idx, model)
handler = protect_signal_handler(handler)
self.connect(view, SIGNAL("clicked(QModelIndex)"), handler)
self.connect(self.reintegrateButton, SIGNAL("clicked()"),
self.doIntegrate)
self.connect(self.chooseSpectrum, SIGNAL("activated(int)"),
self.spectrumChosen)
if self.offerAbortOption:
self.connect(self.okButton, SIGNAL("clicked()"), self.ok)
self.connect(self.abortButton, SIGNAL("clicked()"), self.abort)
def disconnectModelSignals(self):
self.disconnect(self.model,
SIGNAL("dataChanged(QModelIndex,QModelIndex,PyQt_PyObject)"),
self.dataChanged)
self.menubar.disconnect(self.undoAction, SIGNAL("triggered()"),\
protect_signal_handler(self.model.undoLastAction))
self.menubar.disconnect(self.redoAction, SIGNAL("triggered()"),\
protect_signal_handler(self.model.redoLastAction))
def connectModelSignals(self):
self.connect(self.model,
SIGNAL("dataChanged(QModelIndex,QModelIndex,PyQt_PyObject)"),
self.dataChanged)
self.menubar.connect(self.undoAction, SIGNAL("triggered()"),\
protect_signal_handler(self.model.undoLastAction))
self.menubar.connect(self.redoAction, SIGNAL("triggered()"),\
protect_signal_handler(self.model.redoLastAction))
def updateMenubar(self):
undoInfo = self.model.infoLastAction()
redoInfo = self.model.infoRedoAction()
self.undoAction.setEnabled(undoInfo != None)
self.redoAction.setEnabled(redoInfo != None)
if undoInfo:
self.undoAction.setText("Undo: %s" % undoInfo)
if redoInfo:
self.redoAction.setText("Redo: %s" % redoInfo)
def setupViewForTable(self, i):
for j, action in enumerate(self.chooseTableActions):
txt = str(action.text()) # QString -> Python str
if txt.startswith("*"):
txt = " "+txt[1:]
action.setText(txt)
if i==j:
action.setText("*"+txt[1:])
for j in range(len(self.models)):
self.tableViews[j].setVisible(i==j)
if self.model is not None:
self.disconnectModelSignals()
self.model = self.models[i]
self.tableView = self.tableViews[i]
self.setupModelDependendLook()
if self.isIntegrated:
self.model.setNonEditable("method", ["area", "rmse", "method",\
"params"])
self.choosePostfix.clear()
mod = self.model
for p in mod.table.supportedPostfixes(mod.integrationColNames()):
self.choosePostfix.addItem(repr(p))
if len(self.choosePostfix) == 1:
self.choosePostfix.setVisible(False)
self.connectModelSignals()
self.updateMenubar()
@protect_signal_handler
def dataChanged(self, ix1, ix2, src):
minr, maxr = sorted((ix1.row(), ix2.row()))
minc, maxc = sorted((ix1.column(), ix2.column()))
for r in range(minr, maxr+1):
for c in range(minc, maxc+1):
idx = self.model.createIndex(r, c)
self.tableView.update(idx)
if self.hasFeatures:
minr, maxr = sorted((ix1.row(), ix2.row()))
if minr <= self.currentRowIdx <= maxr:
if isinstance(src, IntegrateAction):
self.updatePlots(reset=False)
else:
self.updatePlots(reset=True)
@protect_signal_handler
def abort(self):
self.result = 1
self.close()
@protect_signal_handler
def ok(self):
self.result = 0
self.close()
@protect_signal_handler
def openContextMenu(self, point):
idx = self.tableView.verticalHeader().logicalIndexAt(point)
menu = QMenu()
cloneAction = menu.addAction("Clone row")
removeAction = menu.addAction("Delete row")
undoInfo = self.model.infoLastAction()
redoInfo = self.model.infoRedoAction()
if undoInfo is not None:
undoAction = menu.addAction("Undo %s" % undoInfo)
if redoInfo is not None:
redoAction = menu.addAction("Redo %s" % redoInfo)
appearAt = self.tableView.verticalHeader().mapToGlobal(point)
choosenAction = menu.exec_(appearAt)
if choosenAction == removeAction:
self.model.removeRow(idx)
elif choosenAction == cloneAction:
self.model.cloneRow(idx)
elif undoInfo is not None and choosenAction == undoAction:
self.model.undoLastAction()
elif redoInfo is not None and choosenAction == redoAction:
self.model.redoLastAction()
@protect_signal_handler
def doIntegrate(self):
if self.currentRowIdx < 0:
return # no row selected
# QString -> Python str:
method = str(self.chooseIntMethod.currentText())
# Again QString -> Python str.
# For better readibilty we put single quotes around the postfix
# entry in the QComboBox which we have to remove now:
postfix = str(self.choosePostfix.currentText()).strip("'")
rtmin, rtmax = self.rtPlotter.getRangeSelectionLimits()
self.model.integrate(postfix, self.currentRowIdx, method, rtmin, rtmax)
@protect_signal_handler
def rowClicked(self, rowIdx):
if not self.hasFeatures:
return
self.currentRowIdx = rowIdx
self.rtPlotter.setEnabled(True)
self.updatePlots(reset=True)
if self.hasFeatures:
self.setupSpectrumChooser()
def setupSpectrumChooser(self):
# delete QComboBox:
while self.chooseSpectrum.count():
self.chooseSpectrum.removeItem(0)
# get current spectra
rowidx = self.currentRowIdx
postfixes, spectra = self.model.getLevelNSpectra(rowidx, minLevel=2)
self.currentLevelNSpecs = []
if not len(spectra):
self.chooseSpectrum.setVisible(False)
return
self.chooseSpectrum.setVisible(True)
self.chooseSpectrum.addItem("Show only Level 1 spectra")
for postfix, s in zip(postfixes, spectra):
if postfix != "":
txt = postfix+", "
else:
txt = ""
txt += "rt=%.2fm, level=%d" % (s.rt/60.0, s.msLevel)
mzs = [ mz for (mz, I) in s.precursors ]
precursors = ", ".join("%.6f" % mz for mz in mzs)
if precursors:
txt += ", precursor mzs=[%s]" % precursors
self.chooseSpectrum.addItem(txt)
self.currentLevelNSpecs.append(s)
def updatePlots(self, reset=False):
rowIdx = self.currentRowIdx
eics, mzmin, mzmax, rtmin, rtmax, allrts = self.model.getEics(rowIdx)
curves = eics
configs = configsForEics(eics)
if self.isIntegrated:
smootheds = self.model.getSmoothedEics(rowIdx, allrts)
if smootheds is not None:
curves += smootheds
configs += configsForSmootheds(smootheds)
if not reset:
rtmin, rtmax = self.rtPlotter.getRangeSelectionLimits()
xmin, xmax, ymin, ymax = self.rtPlotter.getLimits()
self.rtPlotter.plot(curves, configs=configs, titles=None,
withmarker=True)
# allrts are sorted !
w = rtmax - rtmin
if w == 0:
w = 30.0 # seconds
self.rtPlotter.setRangeSelectionLimits(rtmin, rtmax)
self.rtPlotter.setXAxisLimits(rtmin -w, rtmax + w)
self.rtPlotter.replot()
if not reset:
self.rtPlotter.setXAxisLimits(xmin, xmax)
self.rtPlotter.setYAxisLimits(ymin, ymax)
self.rtPlotter.updateAxes()
reset = reset and mzmin is not None and mzmax is not None
limits = (mzmin, mzmax) if reset else None
self.plotMz(resetLimits=limits)
@protect_signal_handler
def spectrumChosen(self, idx):
if idx==0:
self.rtPlotter.setEnabled(True)
self.chooseIntMethod.setEnabled(True)
self.reintegrateButton.setEnabled(True)
self.plotMz()
else:
self.rtPlotter.setEnabled(False)
self.chooseIntMethod.setEnabled(False)
self.reintegrateButton.setEnabled(False)
self.mzPlotter.plot([self.currentLevelNSpecs[idx-1].peaks])
self.mzPlotter.resetAxes()
self.mzPlotter.replot()
def plotMz(self, resetLimits=None):
""" this one is used from updatePlots and the rangeselectors
callback """
rtmin=self.rtPlotter.minRTRangeSelected
rtmax=self.rtPlotter.maxRTRangeSelected
# get spectra for current row in given rt-range:
peakmaps = self.model.getPeakmaps(self.currentRowIdx)
peaks = [pm.getDominatingPeakmap().ms1Peaks(rtmin, rtmax) for pm in peakmaps]
# plot peaks
configs = configsForSpectra(peaks)
postfixes = self.model.table.supportedPostfixes(self.model.eicColNames())
titles = map(repr, postfixes)
self.mzPlotter.plot(peaks, configs, titles if len(titles)>1 else None)
if resetLimits:
mzmin, mzmax = resetLimits
Imaxes = []
for p in peaks:
imin = p[:,0].searchsorted(mzmin)
imax = p[:,0].searchsorted(mzmax, side='right')
found = p[imin:imax,1]
if len(found):
Imaxes.append(found.max())
if len(Imaxes) == 0:
Imax = 1.0
else:
Imax = max(Imaxes) * 1.2
self.mzPlotter.setXAxisLimits(mzmin, mzmax)
self.mzPlotter.reset_y_limits(0, Imax)
# plot() needs replot() afterwards !
self.mzPlotter.replot()
