def _setupUi(self):
# self.stop = QToolButton()
# self.stop.setIcon(QIcon('gui/icons/tools_wizard.png'))
# self.stop.setToolTip('Enable or disable the appearance of the contextMenu')
layout = QVBoxLayout(self)
self.smoothButton = QToolButton()
#self.smoothButton.setToolButtonStyle(2)
self.smoothButton.setPopupMode(2)
self.smoothButton.setToolTip("Smooth the visualized data")
#self.smoothButton.setText("Smooth...")
self.smoothButton.setIcon(
QIcon(os.path.normcase('gui/icons/smooth.png')))
self.smoothMenu = QMenu()
self.connect(self.smoothMenu, SIGNAL('triggered(QAction*)'),
self.smooth)
self.smoothButton.setMenu(self.smoothMenu)
self.pw.plotItem.toolBar.addWidget(self.smoothButton)
self.flipButton = QToolButton()
#self.flipButton.setToolButtonStyle(2)
self.flipButton.setIcon(QIcon(os.path.normcase('gui/icons/flip.png')))
self.flipButton.setToolTip("Flip the visualized data")
#self.flipButton.setText("Flip...")
self.flipButton.setPopupMode(2)
self.flipMenu = QMenu()
self.connect(self.flipMenu, SIGNAL('triggered(QAction*)'), self.flip)
self.flipButton.setMenu(self.flipMenu)
self.pw.plotItem.toolBar.addWidget(self.flipButton)
self.annotButton = QToolButton()
#self.annotButton.setToolButtonStyle(2)
self.annotButton.setPopupMode(2)
#self.annotButton.setText("&Annotate...")
self.annotButton.setIcon(
QIcon(os.path.normcase('gui/icons/attach.png')))
self.annotMenu = QMenu()
self.annotMenu.addAction("&Add Annotation")
self.annotMenu.addAction("&Remove last Annotation")
self.annotMenu.addAction("&Remove All Annotation")
self.annotButton.setMenu(self.annotMenu)
self.connect(self.annotMenu.actions()[0], SIGNAL("triggered()"),
self.annotate)
self.connect(self.annotMenu.actions()[1], SIGNAL("triggered()"),
self.removeLastAnnot)
self.connect(self.annotMenu.actions()[2], SIGNAL("triggered()"),
self.removeAllAnnot)
self.pw.plotItem.toolBar.addWidget(self.annotButton)
self.addPlotButton = QToolButton()
#self.addPlotButton.setToolButtonStyle(2)
self.addPlotButton.setText("Add...")
self.addPlotButton.setIcon(
QIcon(os.path.normcase('gui/icons/list_add.png')))
self.addPlotButton.setToolTip("Add a new plot to the current figure")
#self.addPlotButton.setText('&Add Plot')
self.pw.plotItem.toolBar.addWidget(self.addPlotButton)
self.showSpectra = QToolButton()
self.showSpectra.setPopupMode(2) #instant popup
#self.showSpectra.setToolButtonStyle(2)
self.showSpectra.setIcon(
QIcon(os.path.normcase('gui/icons/file_export.png')))
#self.showSpectra.setText('&Show /hide...')
self.showSpectra.setToolTip('Show/hide ...')
self.showMenu = QMenu()
self.showTextLabels = QAction("&Show Labels", self.showMenu)
self.showTextLabels.setCheckable(True)
self.showTextLabels.setChecked(True)
self.showMenu.addAction(self.showTextLabels)
self.connect(self.showMenu.actions()[0], SIGNAL('toggled(bool)'),
self.setTextLabelsVisibility)
showSpectrum = QAction("&Merged Spectrum", self.showMenu)
showSpectrum.setCheckable(True)
if self.flags == 'chroma' or self.flags == 'spectra':
showSpectrum.setEnabled(False)
self.showMenu.addAction(showSpectrum)
self.connect(self.showMenu.actions()[1], SIGNAL('toggled(bool)'),
self.drawSpectraRequested)
showNonXCMSPeak = QAction("&Show Non XCMS Peak", self.showMenu)
showNonXCMSPeak.setCheckable(True)
if self.flags == 'spectra':
showNonXCMSPeak.setEnabled(False)
self.showMenu.addAction(showNonXCMSPeak)
self.connect(self.showMenu.actions()[2], SIGNAL('toggled(bool)'),
self.setPixmapVisibility)
showDataPoints = QAction("&Show DataPoints", self.showMenu)
showDataPoints.setCheckable(True)
showDataPoints.setChecked(False)
self.showMenu.addAction(showDataPoints)
self.connect(self.showMenu.actions()[3], SIGNAL('toggled(bool)'),
self.setDataPointsVisibility)
self.showSpectra.setMenu(self.showMenu)
self.pw.plotItem.toolBar.addWidget(self.showSpectra)
self.saveToPng = QToolButton()
self.saveToPng.setIcon(
QIcon(os.path.normcase('gui/icons/thumbnail.png')))
#self.saveToPng.setToolButtonStyle(2)
#self.saveToPng.setText("Save to Png...")
self.pw.plotItem.toolBar.addWidget(self.saveToPng)
self.connect(self.saveToPng, SIGNAL('clicked()'), self.pw.writeImage)
#add bar plot even if we are plotting chroma
#cause we can find non xcms peaks
self.barPlot = BarPlot(scene=self.pw.sceneObj)
#self.barPlot.rotate(-90.)
if self.flags == 'peak':
self.barPlot.setPeakGroup(self.data)
#TODO modify to get this close to us
#on the left part
xpos = self.barPlot.scene().width() * 3.5 #-bwidth;
ypos = self.barPlot.scene().height() * 1.1
self.barPlot.setPos(xpos, ypos)
self.barPlot.setZValue(1000)
layout.addWidget(self.pw)
layout.addWidget(self.pw.plotItem.toolBar)
def _setupUi (self):
# self.stop = QToolButton()
# self.stop.setIcon(QIcon('gui/icons/tools_wizard.png'))
# self.stop.setToolTip('Enable or disable the appearance of the contextMenu')
layout=QVBoxLayout(self)
self.smoothButton=QToolButton()
#self.smoothButton.setToolButtonStyle(2)
self.smoothButton.setPopupMode(2)
self.smoothButton.setToolTip("Smooth the visualized data")
#self.smoothButton.setText("Smooth...")
self.smoothButton.setIcon(QIcon(os.path.normcase('gui/icons/smooth.png')))
self.smoothMenu = QMenu()
self.connect(self.smoothMenu, SIGNAL('triggered(QAction*)'), self.smooth)
self.smoothButton.setMenu(self.smoothMenu)
self.pw.plotItem.toolBar.addWidget(self.smoothButton)
self.flipButton=QToolButton()
#self.flipButton.setToolButtonStyle(2)
self.flipButton.setIcon(QIcon(os.path.normcase('gui/icons/flip.png')))
self.flipButton.setToolTip("Flip the visualized data")
#self.flipButton.setText("Flip...")
self.flipButton.setPopupMode(2)
self.flipMenu = QMenu()
self.connect(self.flipMenu, SIGNAL('triggered(QAction*)'), self.flip)
self.flipButton.setMenu(self.flipMenu)
self.pw.plotItem.toolBar.addWidget(self.flipButton)
self.annotButton=QToolButton()
#self.annotButton.setToolButtonStyle(2)
self.annotButton.setPopupMode(2)
#self.annotButton.setText("&Annotate...")
self.annotButton.setIcon(QIcon(os.path.normcase('gui/icons/attach.png')))
self.annotMenu = QMenu()
self.annotMenu.addAction("&Add Annotation")
self.annotMenu.addAction("&Remove last Annotation")
self.annotMenu.addAction("&Remove All Annotation")
self.annotButton.setMenu(self.annotMenu)
self.connect(self.annotMenu.actions()[0], SIGNAL("triggered()"), self.annotate)
self.connect(self.annotMenu.actions()[1], SIGNAL("triggered()"), self.removeLastAnnot)
self.connect(self.annotMenu.actions()[2], SIGNAL("triggered()"), self.removeAllAnnot)
self.pw.plotItem.toolBar.addWidget(self.annotButton)
self.addPlotButton=QToolButton()
#self.addPlotButton.setToolButtonStyle(2)
self.addPlotButton.setText("Add...")
self.addPlotButton.setIcon(QIcon(os.path.normcase('gui/icons/list_add.png')))
self.addPlotButton.setToolTip("Add a new plot to the current figure")
#self.addPlotButton.setText('&Add Plot')
self.pw.plotItem.toolBar.addWidget(self.addPlotButton)
self.showSpectra=QToolButton()
self.showSpectra.setPopupMode(2) #instant popup
#self.showSpectra.setToolButtonStyle(2)
self.showSpectra.setIcon(QIcon(os.path.normcase('gui/icons/file_export.png')))
#self.showSpectra.setText('&Show /hide...')
self.showSpectra.setToolTip('Show/hide ...')
self.showMenu=QMenu()
self.showTextLabels=QAction("&Show Labels", self.showMenu)
self.showTextLabels.setCheckable(True)
self.showTextLabels.setChecked(True)
self.showMenu.addAction(self.showTextLabels)
self.connect(self.showMenu.actions()[0], SIGNAL('toggled(bool)'), self.setTextLabelsVisibility)
showSpectrum=QAction("&Merged Spectrum", self.showMenu)
showSpectrum.setCheckable(True)
if self.flags == 'chroma' or self.flags == 'spectra':
showSpectrum.setEnabled(False)
self.showMenu.addAction(showSpectrum)
self.connect(self.showMenu.actions()[1], SIGNAL('toggled(bool)'), self.drawSpectraRequested)
showNonXCMSPeak=QAction("&Show Non XCMS Peak", self.showMenu)
showNonXCMSPeak.setCheckable(True)
if self.flags == 'spectra':
showNonXCMSPeak.setEnabled(False)
self.showMenu.addAction(showNonXCMSPeak)
self.connect(self.showMenu.actions()[2],
SIGNAL('toggled(bool)'),
self.setPixmapVisibility)
showDataPoints = QAction("&Show DataPoints", self.showMenu)
showDataPoints.setCheckable(True)
showDataPoints.setChecked(False)
self.showMenu.addAction(showDataPoints)
self.connect(self.showMenu.actions()[3],
SIGNAL('toggled(bool)'),
self.setDataPointsVisibility)
self.showSpectra.setMenu(self.showMenu)
self.pw.plotItem.toolBar.addWidget(self.showSpectra)
self.saveToPng = QToolButton()
self.saveToPng.setIcon(QIcon(os.path.normcase('gui/icons/thumbnail.png')))
#self.saveToPng.setToolButtonStyle(2)
#self.saveToPng.setText("Save to Png...")
self.pw.plotItem.toolBar.addWidget(self.saveToPng)
self.connect(self.saveToPng, SIGNAL('clicked()'), self.pw.writeImage)
#add bar plot even if we are plotting chroma
#cause we can find non xcms peaks
self.barPlot = BarPlot(scene=self.pw.sceneObj)
#self.barPlot.rotate(-90.)
if self.flags == 'peak':
self.barPlot.setPeakGroup(self.data)
#TODO modify to get this close to us
#on the left part
xpos = self.barPlot.scene().width()*3.5#-bwidth;
ypos = self.barPlot.scene().height()*1.1
self.barPlot.setPos(xpos,ypos)
self.barPlot.setZValue(1000)
layout.addWidget(self.pw)
layout.addWidget(self.pw.plotItem.toolBar)
class MSQtCanvas(QWidget, MSDialogController):
"""
DONE:the current peak is not updated while the user press up and down key on the treeView
TODO: think about a mjor redesign of those classes
"""
#linePlotted = pyqtSignal(object, str)
#lineRemoved = pyqtSignal(object)
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 getMax(self):
localXmin = []
localXmax = []
localYmax = []
for el in self.data:
if el is None:
continue
localXmin.append(min_f(el.x_data))
localXmax.append(max_f(el.x_data))
localYmax.append(max_l(el.y_data))
return min_f(np.array(localXmin)), max_f(np.array(localXmax)), max_l(
np.array(localYmax))
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 drawEics(self, data):
for chrom in data:
color = QColor.fromRgbF(*(chrom.sample.color + (.5, )))
c = self.pw.plotItem.plot(x=chrom.x_data,
y=chrom.y_data,
pen=color)
#c = Line(chrom.x_data, chrom.y_data,
# color,
# parent=self.pw.plotItem.vb,
# scene=self.pw.scene())
self.drawnItems[chrom.sample] = c
#self.pw.addItem(c)
#self.pw.plotItem.curves.append(c)
self.emit(SIGNAL('linePlotted'), chrom.sample.shortName())
if self.flags != 'peaks':
self.pw.autoRange()
#===========================================================================
# UI stuffs
#===========================================================================
def _setupUi(self):
# self.stop = QToolButton()
# self.stop.setIcon(QIcon('gui/icons/tools_wizard.png'))
# self.stop.setToolTip('Enable or disable the appearance of the contextMenu')
layout = QVBoxLayout(self)
self.smoothButton = QToolButton()
#self.smoothButton.setToolButtonStyle(2)
self.smoothButton.setPopupMode(2)
self.smoothButton.setToolTip("Smooth the visualized data")
#self.smoothButton.setText("Smooth...")
self.smoothButton.setIcon(
QIcon(os.path.normcase('gui/icons/smooth.png')))
self.smoothMenu = QMenu()
self.connect(self.smoothMenu, SIGNAL('triggered(QAction*)'),
self.smooth)
self.smoothButton.setMenu(self.smoothMenu)
self.pw.plotItem.toolBar.addWidget(self.smoothButton)
self.flipButton = QToolButton()
#self.flipButton.setToolButtonStyle(2)
self.flipButton.setIcon(QIcon(os.path.normcase('gui/icons/flip.png')))
self.flipButton.setToolTip("Flip the visualized data")
#self.flipButton.setText("Flip...")
self.flipButton.setPopupMode(2)
self.flipMenu = QMenu()
self.connect(self.flipMenu, SIGNAL('triggered(QAction*)'), self.flip)
self.flipButton.setMenu(self.flipMenu)
self.pw.plotItem.toolBar.addWidget(self.flipButton)
self.annotButton = QToolButton()
#self.annotButton.setToolButtonStyle(2)
self.annotButton.setPopupMode(2)
#self.annotButton.setText("&Annotate...")
self.annotButton.setIcon(
QIcon(os.path.normcase('gui/icons/attach.png')))
self.annotMenu = QMenu()
self.annotMenu.addAction("&Add Annotation")
self.annotMenu.addAction("&Remove last Annotation")
self.annotMenu.addAction("&Remove All Annotation")
self.annotButton.setMenu(self.annotMenu)
self.connect(self.annotMenu.actions()[0], SIGNAL("triggered()"),
self.annotate)
self.connect(self.annotMenu.actions()[1], SIGNAL("triggered()"),
self.removeLastAnnot)
self.connect(self.annotMenu.actions()[2], SIGNAL("triggered()"),
self.removeAllAnnot)
self.pw.plotItem.toolBar.addWidget(self.annotButton)
self.addPlotButton = QToolButton()
#self.addPlotButton.setToolButtonStyle(2)
self.addPlotButton.setText("Add...")
self.addPlotButton.setIcon(
QIcon(os.path.normcase('gui/icons/list_add.png')))
self.addPlotButton.setToolTip("Add a new plot to the current figure")
#self.addPlotButton.setText('&Add Plot')
self.pw.plotItem.toolBar.addWidget(self.addPlotButton)
self.showSpectra = QToolButton()
self.showSpectra.setPopupMode(2) #instant popup
#self.showSpectra.setToolButtonStyle(2)
self.showSpectra.setIcon(
QIcon(os.path.normcase('gui/icons/file_export.png')))
#self.showSpectra.setText('&Show /hide...')
self.showSpectra.setToolTip('Show/hide ...')
self.showMenu = QMenu()
self.showTextLabels = QAction("&Show Labels", self.showMenu)
self.showTextLabels.setCheckable(True)
self.showTextLabels.setChecked(True)
self.showMenu.addAction(self.showTextLabels)
self.connect(self.showMenu.actions()[0], SIGNAL('toggled(bool)'),
self.setTextLabelsVisibility)
showSpectrum = QAction("&Merged Spectrum", self.showMenu)
showSpectrum.setCheckable(True)
if self.flags == 'chroma' or self.flags == 'spectra':
showSpectrum.setEnabled(False)
self.showMenu.addAction(showSpectrum)
self.connect(self.showMenu.actions()[1], SIGNAL('toggled(bool)'),
self.drawSpectraRequested)
showNonXCMSPeak = QAction("&Show Non XCMS Peak", self.showMenu)
showNonXCMSPeak.setCheckable(True)
if self.flags == 'spectra':
showNonXCMSPeak.setEnabled(False)
self.showMenu.addAction(showNonXCMSPeak)
self.connect(self.showMenu.actions()[2], SIGNAL('toggled(bool)'),
self.setPixmapVisibility)
showDataPoints = QAction("&Show DataPoints", self.showMenu)
showDataPoints.setCheckable(True)
showDataPoints.setChecked(False)
self.showMenu.addAction(showDataPoints)
self.connect(self.showMenu.actions()[3], SIGNAL('toggled(bool)'),
self.setDataPointsVisibility)
self.showSpectra.setMenu(self.showMenu)
self.pw.plotItem.toolBar.addWidget(self.showSpectra)
self.saveToPng = QToolButton()
self.saveToPng.setIcon(
QIcon(os.path.normcase('gui/icons/thumbnail.png')))
#self.saveToPng.setToolButtonStyle(2)
#self.saveToPng.setText("Save to Png...")
self.pw.plotItem.toolBar.addWidget(self.saveToPng)
self.connect(self.saveToPng, SIGNAL('clicked()'), self.pw.writeImage)
#add bar plot even if we are plotting chroma
#cause we can find non xcms peaks
self.barPlot = BarPlot(scene=self.pw.sceneObj)
#self.barPlot.rotate(-90.)
if self.flags == 'peak':
self.barPlot.setPeakGroup(self.data)
#TODO modify to get this close to us
#on the left part
xpos = self.barPlot.scene().width() * 3.5 #-bwidth;
ypos = self.barPlot.scene().height() * 1.1
self.barPlot.setPos(xpos, ypos)
self.barPlot.setZValue(1000)
layout.addWidget(self.pw)
layout.addWidget(self.pw.plotItem.toolBar)
def showTextLabel(self, x, y, secure=25):
"""
add labels of principle peaks of spectrum or chroma
on the plot, return the labels, that we can show hide
"""
maxis = [] #will contain tuple(rt, intens)
indexes = []
#from core.MetObjects import MSAbstractTypes
from scipy.ndimage import gaussian_filter1d as gauss
z = gauss(y, 1)
#z = MSAbstractTypes.computeBaseLine(z, 92., 0.8)
i = 0
while i < len(z) - 1:
while z[i + 1] >= z[i] and i < len(y) - 2:
i += 1
maxis.append((x[i], y[i]))
indexes.append(i)
while z[i + 1] <= z[i] and i < len(z) - 2:
i += 1
i += 1
labels = []
for t in sorted(maxis, key=lambda x: x[1])[-5:]:
g = QGraphicsTextItem(str(t[0]))
g.setFlag(QGraphicsItem.ItemIgnoresTransformations)
font = QApplication.font()
font.setPointSizeF(6.5)
g.setFont(font)
g.setDefaultTextColor(Qt.black)
g.setPos(t[0], t[1])
labels.append(g)
self.pw.addItem(g)
return labels
#===============================================================================
#SLOTS
#===============================================================================
def redrawAll(self, value):
self.pw.clear()
self._plotting(self.data)
def disHighlightOne(self, idx):
if not idx.isValid():
return
sample = self.model.sample(idx.data().toString(), fullNameEntry=False)
if sample is None:
return
try:
self.drawnItems[sample].setHighlighted(False)
except KeyError:
pass
def highlight(self, idx):
if not idx.isValid():
return
sample = self.model.sample(idx.data().toString(), fullNameEntry=False)
if sample is None:
return
try:
self.drawnItems[sample].setHighlighted(True)
except KeyError:
pass
#print "sample not found"
self.pw.plotItem.update() #works
def disHighlight(self):
for key in self.drawnItems.iterkeys():
self.drawnItems[key].setHighlighted(False)
self.pw.plotItem.update()
def setTextLabelsVisibility(self, bool_):
for t in self.textLabels:
t.setVisible(bool_)
def setDataPointsVisibility(self, b):
if self.dataPoints is None:
if self.flags == 'peak':
chrom = self.ref.sample.massExtraction(self.ref.mass(),
self.ref.sample.ppm,
asChromatogram=True)
self.dataPoints = ScatterPlotItem(x=chrom.x_data,
y=chrom.y_data)
else:
self.dataPoints = ScatterPlotItem(x=self.ref.x_data,
y=self.ref.y_data)
if self.flags != 'spectra':
self.dataPoints.sigClicked.connect(self.requestSpectra)
self.pw.addDataItem(self.dataPoints)
self.dataPoints.setVisible(b)
def setPixmapVisibility(self, bool_):
"""
draw other peaks than the xcms peak
"""
if not self.pixmaps and bool_:
ppm = 1. if self.ref.sample.kind == 'MRM' else self.ref.sample.ppm
chrom = self.ref.sample.massExtraction(self.ref.mass(), ppm, asChromatogram=True) \
if self.flags == 'peak' else self.ref
chrom.findNonXCMSPeaks()
for p in chrom.peaks.ipeaks():
if self.flags == 'peak':
diff = (p.height * 10) / 100
if abs(p.height - self.ref.height) < diff:
continue #we assume that they are the same peaks
pix = PeakIndicator(p, icon='flags')
#self.connect(pix, SIGNAL("highlightRequested"), c.setHighlighted)
self.connect(pix, SIGNAL('updateBarPlot'),
self.barPlot.setPeakGroup)
pix.setPos(p.rt, p.height + (p.height * 10) / 100.)
pix.setZValue(1000)
self.pixmaps.append(pix)
self.pw.addItem(pix)
if self.pixmaps:
for t in self.pixmaps:
t.setVisible(bool_)
@pyqtSlot()
def updateCurrentPeak(self):
idx = self.acTree.selectedIndexes()[0]
s = self.model.sample(idx.parent().data().toString(),
fullNameEntry=False)
if s is not None:
self.currentPeak = s.peakAt(*map(float,
idx.data().toString().split('/')))
def requestSpectra(self, scatter, l):
"""
idea plot all spectra between a time range
and not only with only one spectra
"""
if not l:
return
ref = l[0]
self.emit(SIGNAL("drawSpectrumByTime"), ref.pos(), self.ref.sample)
@pyqtSlot()
def drawSpectraRequested(self, bool_):
"""
i think this is for plotting merged spectrum
"""
if bool_:
self.emit(SIGNAL('drawSpectraRequested'), self.currentPeak)
else:
self.hideRequested()
def drawSpectra(self, l):
self.emit(
SIGNAL('drawSpectra(PyQt_PyObject, PyQt_PyObject, PyQt_PyObject)'),
l[0], l[1], self.ref.sample)
@pyqtSlot()
def hideRequested(self):
self.emit(SIGNAL('hideRequested'))
self.showMenu.actions()[1].setChecked(False)
@pyqtSlot()
def redraw(self):
"""
this is for updating the view port
when hiding or not samples
"""
chromas = []
for spl in self.model:
if spl.checked:
if spl in self.drawnItems.keys():
self.drawnItems[spl].setVisible(True)
else:
chromas.append(spl.chroma[0])
else:
self.drawnItems[spl].setVisible(False)
self._plotting(chromas)
self.pw.plotItem.update() #works
def cleanScene(self):
"""
remove all items in the trash
"""
for element in self.trashItems:
self.pw.sceneObj.removeItem(element)
@pyqtSlot()
def updateContextMenu(self, line):
self.flipMenu.addAction(line)
self.smoothMenu.addAction(line)
#===============================================================================
# CONTEXT MENU SLOTS
#===============================================================================
@pyqtSlot(str)
def flip(self, action):
spl = self.model.sample(self.fullXmlPath(action.text()))
if spl is None:
print "can not flip, can not recognize the selected sample"
return
try:
self.drawnItems[spl].updateData(-self.drawnItems[spl].getData()[1],
self.drawnItems[spl].getData()[0])
except KeyError:
pass
if len(self.data) == 1:
#we are flipping the text labels only
#if only one dataset is flipped
for item in self.textLabels:
item.setPos(item.pos().x(), -item.pos().y())
@pyqtSlot(str)
def smooth(self, action):
"""
TODO:
would be good to reuse the widget in the menuControl
"""
from core.MetObjects import MSAbstractTypes
class Dial(QDialog):
choices = ['flat', 'hanning', 'hamming', 'bartlett', 'blackman']
def __init__(self, parent):
QDialog.__init__(self, parent)
f = QFormLayout(self)
self.a = QSpinBox(self)
self.a.setValue(30)
self.b = QComboBox(self)
self.b.addItems(self.choices)
self.c = QDialogButtonBox(self)
self.c.setStandardButtons(QDialogButtonBox.Cancel
| QDialogButtonBox.Ok)
f.addRow("window:", self.a)
f.addRow("method:", self.b)
f.addRow("", self.c)
self.connect(self.c, SIGNAL("accepted()"), self.sendData)
self.connect(self.c, SIGNAL("rejected()"), self.reinitialize)
def sendData(self):
self.parent().window = self.a.value()
self.parent().method = self.b.currentText()
self.close()
def reinitialize(self):
self.parent().window = None
self.parent().method = None
self.close()
Dial(self).exec_()
if self.window and self.method:
for spl in self.drawnItems.keys():
if action.text() == spl.shortName():
self.drawnItems[spl].updateData(
MSAbstractTypes.averageSmoothing(
self.drawnItems[spl].getData()[1], self.window,
self.method), self.drawnItems[spl].getData()[0])
@pyqtSlot()
def plotEIC(self):
if self.flags == 'spectra':
#show double combobox
#select the good spectra then draw
pass
else:
mass, ok = QInputDialog.getText(self.view, "EIC query", "mass:")
if not (mass and ok):
return
xmlfile = self.fullXmlPath(self.selection[0].data().toString())
if not xmlfile:
xmlfile = self.fullXmlPath(
self.selection[0].parent().data().toString())
if not xmlfile:
print "item clicked not recognized..."
return
sample = self.model.sample(xmlfile)
if sample.kind == 'HighRes':
error = (sample.ppm / 1e6) * float(mass)
x, y = massExtraction(sample, float(mass), error)
from core.MetObjects import MSChromatogram
chrom = MSChromatogram(x_data=x, y_data=y, sample=sample)
else:
chrom = sample.getChromWithTrans(math.ceil(float(mass)))
self.view.addMdiSubWindow(
MSQtCanvas([chrom],
"EIC %s" % str(mass),
labels={
'bottom': 'RT(s)',
'left': 'INTENSITY'
}))
#===========================================================================
# annotate stuff
#===========================================================================
@pyqtSlot()
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 removeAllAnnot(self):
if not self.trashItems:
self.view.showErrorMessage("Error", "No annotation detected")
return
for i in self.trashItems:
self.pw.removeItem(i)
def removeLastAnnot(self):
if not self.trashItems:
self.view.showErrorMessage("Error", "No annotation detected")
self.pw.removeItem(self.trashItems[-1])
class MSQtCanvas(QWidget, MSDialogController):
"""
DONE:the current peak is not updated while the user press up and down key on the treeView
TODO: think about a mjor redesign of those classes
"""
#linePlotted = pyqtSignal(object, str)
#lineRemoved = pyqtSignal(object)
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 getMax(self):
localXmin =[]
localXmax = []
localYmax = []
for el in self.data:
if el is None:
continue
localXmin.append(min_f(el.x_data))
localXmax.append(max_f(el.x_data))
localYmax.append(max_l(el.y_data))
return min_f(np.array(localXmin)), max_f(np.array(localXmax)), max_l(np.array(localYmax))
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 drawEics(self, data):
for chrom in data:
color = QColor.fromRgbF(*(chrom.sample.color+(.5,)))
c=self.pw.plotItem.plot(x=chrom.x_data, y=chrom.y_data, pen=color)
#c = Line(chrom.x_data, chrom.y_data,
# color,
# parent=self.pw.plotItem.vb,
# scene=self.pw.scene())
self.drawnItems[chrom.sample] = c
#self.pw.addItem(c)
#self.pw.plotItem.curves.append(c)
self.emit(SIGNAL('linePlotted'), chrom.sample.shortName())
if self.flags != 'peaks':
self.pw.autoRange()
#===========================================================================
# UI stuffs
#===========================================================================
def _setupUi (self):
# self.stop = QToolButton()
# self.stop.setIcon(QIcon('gui/icons/tools_wizard.png'))
# self.stop.setToolTip('Enable or disable the appearance of the contextMenu')
layout=QVBoxLayout(self)
self.smoothButton=QToolButton()
#self.smoothButton.setToolButtonStyle(2)
self.smoothButton.setPopupMode(2)
self.smoothButton.setToolTip("Smooth the visualized data")
#self.smoothButton.setText("Smooth...")
self.smoothButton.setIcon(QIcon(os.path.normcase('gui/icons/smooth.png')))
self.smoothMenu = QMenu()
self.connect(self.smoothMenu, SIGNAL('triggered(QAction*)'), self.smooth)
self.smoothButton.setMenu(self.smoothMenu)
self.pw.plotItem.toolBar.addWidget(self.smoothButton)
self.flipButton=QToolButton()
#self.flipButton.setToolButtonStyle(2)
self.flipButton.setIcon(QIcon(os.path.normcase('gui/icons/flip.png')))
self.flipButton.setToolTip("Flip the visualized data")
#self.flipButton.setText("Flip...")
self.flipButton.setPopupMode(2)
self.flipMenu = QMenu()
self.connect(self.flipMenu, SIGNAL('triggered(QAction*)'), self.flip)
self.flipButton.setMenu(self.flipMenu)
self.pw.plotItem.toolBar.addWidget(self.flipButton)
self.annotButton=QToolButton()
#self.annotButton.setToolButtonStyle(2)
self.annotButton.setPopupMode(2)
#self.annotButton.setText("&Annotate...")
self.annotButton.setIcon(QIcon(os.path.normcase('gui/icons/attach.png')))
self.annotMenu = QMenu()
self.annotMenu.addAction("&Add Annotation")
self.annotMenu.addAction("&Remove last Annotation")
self.annotMenu.addAction("&Remove All Annotation")
self.annotButton.setMenu(self.annotMenu)
self.connect(self.annotMenu.actions()[0], SIGNAL("triggered()"), self.annotate)
self.connect(self.annotMenu.actions()[1], SIGNAL("triggered()"), self.removeLastAnnot)
self.connect(self.annotMenu.actions()[2], SIGNAL("triggered()"), self.removeAllAnnot)
self.pw.plotItem.toolBar.addWidget(self.annotButton)
self.addPlotButton=QToolButton()
#self.addPlotButton.setToolButtonStyle(2)
self.addPlotButton.setText("Add...")
self.addPlotButton.setIcon(QIcon(os.path.normcase('gui/icons/list_add.png')))
self.addPlotButton.setToolTip("Add a new plot to the current figure")
#self.addPlotButton.setText('&Add Plot')
self.pw.plotItem.toolBar.addWidget(self.addPlotButton)
self.showSpectra=QToolButton()
self.showSpectra.setPopupMode(2) #instant popup
#self.showSpectra.setToolButtonStyle(2)
self.showSpectra.setIcon(QIcon(os.path.normcase('gui/icons/file_export.png')))
#self.showSpectra.setText('&Show /hide...')
self.showSpectra.setToolTip('Show/hide ...')
self.showMenu=QMenu()
self.showTextLabels=QAction("&Show Labels", self.showMenu)
self.showTextLabels.setCheckable(True)
self.showTextLabels.setChecked(True)
self.showMenu.addAction(self.showTextLabels)
self.connect(self.showMenu.actions()[0], SIGNAL('toggled(bool)'), self.setTextLabelsVisibility)
showSpectrum=QAction("&Merged Spectrum", self.showMenu)
showSpectrum.setCheckable(True)
if self.flags == 'chroma' or self.flags == 'spectra':
showSpectrum.setEnabled(False)
self.showMenu.addAction(showSpectrum)
self.connect(self.showMenu.actions()[1], SIGNAL('toggled(bool)'), self.drawSpectraRequested)
showNonXCMSPeak=QAction("&Show Non XCMS Peak", self.showMenu)
showNonXCMSPeak.setCheckable(True)
if self.flags == 'spectra':
showNonXCMSPeak.setEnabled(False)
self.showMenu.addAction(showNonXCMSPeak)
self.connect(self.showMenu.actions()[2],
SIGNAL('toggled(bool)'),
self.setPixmapVisibility)
showDataPoints = QAction("&Show DataPoints", self.showMenu)
showDataPoints.setCheckable(True)
showDataPoints.setChecked(False)
self.showMenu.addAction(showDataPoints)
self.connect(self.showMenu.actions()[3],
SIGNAL('toggled(bool)'),
self.setDataPointsVisibility)
self.showSpectra.setMenu(self.showMenu)
self.pw.plotItem.toolBar.addWidget(self.showSpectra)
self.saveToPng = QToolButton()
self.saveToPng.setIcon(QIcon(os.path.normcase('gui/icons/thumbnail.png')))
#self.saveToPng.setToolButtonStyle(2)
#self.saveToPng.setText("Save to Png...")
self.pw.plotItem.toolBar.addWidget(self.saveToPng)
self.connect(self.saveToPng, SIGNAL('clicked()'), self.pw.writeImage)
#add bar plot even if we are plotting chroma
#cause we can find non xcms peaks
self.barPlot = BarPlot(scene=self.pw.sceneObj)
#self.barPlot.rotate(-90.)
if self.flags == 'peak':
self.barPlot.setPeakGroup(self.data)
#TODO modify to get this close to us
#on the left part
xpos = self.barPlot.scene().width()*3.5#-bwidth;
ypos = self.barPlot.scene().height()*1.1
self.barPlot.setPos(xpos,ypos)
self.barPlot.setZValue(1000)
layout.addWidget(self.pw)
layout.addWidget(self.pw.plotItem.toolBar)
def showTextLabel(self, x, y, secure=25):
"""
add labels of principle peaks of spectrum or chroma
on the plot, return the labels, that we can show hide
"""
maxis=[]#will contain tuple(rt, intens)
indexes=[]
#from core.MetObjects import MSAbstractTypes
from scipy.ndimage import gaussian_filter1d as gauss
z=gauss(y, 1)
#z = MSAbstractTypes.computeBaseLine(z, 92., 0.8)
i=0
while i <len(z)-1:
while z[i+1] >= z[i] and i < len(y)-2:
i+=1
maxis.append((x[i], y[i]))
indexes.append(i)
while z[i+1] <= z[i] and i<len(z)-2:
i+=1
i+=1
labels=[]
for t in sorted(maxis, key=lambda x:x[1])[-5:]:
g=QGraphicsTextItem(str(t[0]))
g.setFlag(QGraphicsItem.ItemIgnoresTransformations)
font=QApplication.font()
font.setPointSizeF(6.5)
g.setFont(font)
g.setDefaultTextColor(Qt.black)
g.setPos(t[0], t[1])
labels.append(g)
self.pw.addItem(g)
return labels
#===============================================================================
#SLOTS
#===============================================================================
def redrawAll(self, value):
self.pw.clear()
self._plotting(self.data)
def disHighlightOne(self, idx):
if not idx.isValid():
return
sample = self.model.sample(idx.data().toString(), fullNameEntry=False)
if sample is None:
return
try:
self.drawnItems[sample].setHighlighted(False)
except KeyError:
pass
def highlight(self, idx):
if not idx.isValid():
return
sample = self.model.sample(idx.data().toString(), fullNameEntry=False)
if sample is None:
return
try:
self.drawnItems[sample].setHighlighted(True)
except KeyError:
pass
#print "sample not found"
self.pw.plotItem.update()#works
def disHighlight(self):
for key in self.drawnItems.iterkeys():
self.drawnItems[key].setHighlighted(False)
self.pw.plotItem.update()
def setTextLabelsVisibility(self, bool_):
for t in self.textLabels:
t.setVisible(bool_)
def setDataPointsVisibility(self, b):
if self.dataPoints is None:
if self.flags == 'peak':
chrom = self.ref.sample.massExtraction(self.ref.mass(), self.ref.sample.ppm, asChromatogram=True)
self.dataPoints = ScatterPlotItem(x=chrom.x_data, y=chrom.y_data)
else:
self.dataPoints = ScatterPlotItem(x=self.ref.x_data, y=self.ref.y_data)
if self.flags != 'spectra':
self.dataPoints.sigClicked.connect(self.requestSpectra)
self.pw.addDataItem(self.dataPoints)
self.dataPoints.setVisible(b)
def setPixmapVisibility(self, bool_):
"""
draw other peaks than the xcms peak
"""
if not self.pixmaps and bool_:
ppm = 1. if self.ref.sample.kind=='MRM' else self.ref.sample.ppm
chrom = self.ref.sample.massExtraction(self.ref.mass(), ppm, asChromatogram=True) \
if self.flags == 'peak' else self.ref
chrom.findNonXCMSPeaks()
for p in chrom.peaks.ipeaks():
if self.flags == 'peak':
diff=(p.height*10)/100
if abs(p.height-self.ref.height) < diff:
continue #we assume that they are the same peaks
pix=PeakIndicator(p, icon='flags')
#self.connect(pix, SIGNAL("highlightRequested"), c.setHighlighted)
self.connect(pix, SIGNAL('updateBarPlot'), self.barPlot.setPeakGroup)
pix.setPos(p.rt, p.height + (p.height * 10) / 100.)
pix.setZValue(1000)
self.pixmaps.append(pix)
self.pw.addItem(pix)
if self.pixmaps:
for t in self.pixmaps:
t.setVisible(bool_)
@pyqtSlot()
def updateCurrentPeak(self):
idx=self.acTree.selectedIndexes()[0]
s=self.model.sample(idx.parent().data().toString(), fullNameEntry=False)
if s is not None:
self.currentPeak=s.peakAt(*map(float, idx.data().toString().split('/')))
def requestSpectra(self, scatter, l):
"""
idea plot all spectra between a time range
and not only with only one spectra
"""
if not l:
return
ref = l[0]
self.emit(SIGNAL("drawSpectrumByTime"), ref.pos(), self.ref.sample)
@pyqtSlot()
def drawSpectraRequested(self, bool_):
"""
i think this is for plotting merged spectrum
"""
if bool_:
self.emit(SIGNAL('drawSpectraRequested'), self.currentPeak)
else:
self.hideRequested()
def drawSpectra(self, l):
self.emit(SIGNAL('drawSpectra(PyQt_PyObject, PyQt_PyObject, PyQt_PyObject)'), l[0], l[1], self.ref.sample)
@pyqtSlot()
def hideRequested(self):
self.emit(SIGNAL('hideRequested'))
self.showMenu.actions()[1].setChecked(False)
@pyqtSlot()
def redraw(self):
"""
this is for updating the view port
when hiding or not samples
"""
chromas =[]
for spl in self.model:
if spl.checked:
if spl in self.drawnItems.keys():
self.drawnItems[spl].setVisible(True)
else:
chromas.append(spl.chroma[0])
else:
self.drawnItems[spl].setVisible(False)
self._plotting(chromas)
self.pw.plotItem.update()#works
def cleanScene(self):
"""
remove all items in the trash
"""
for element in self.trashItems:
self.pw.sceneObj.removeItem(element)
@pyqtSlot()
def updateContextMenu(self, line):
self.flipMenu.addAction(line)
self.smoothMenu.addAction(line)
#===============================================================================
# CONTEXT MENU SLOTS
#===============================================================================
@pyqtSlot(str)
def flip(self, action):
spl=self.model.sample(self.fullXmlPath(action.text()))
if spl is None:
print "can not flip, can not recognize the selected sample"
return
try:
self.drawnItems[spl].updateData(-self.drawnItems[spl].getData()[1],
self.drawnItems[spl].getData()[0])
except KeyError:
pass
if len(self.data) == 1:
#we are flipping the text labels only
#if only one dataset is flipped
for item in self.textLabels:
item.setPos(item.pos().x(), -item.pos().y())
@pyqtSlot(str)
def smooth(self, action):
"""
TODO:
would be good to reuse the widget in the menuControl
"""
from core.MetObjects import MSAbstractTypes
class Dial(QDialog):
choices =['flat', 'hanning', 'hamming', 'bartlett', 'blackman']
def __init__(self, parent):
QDialog.__init__(self, parent)
f =QFormLayout(self)
self.a =QSpinBox(self)
self.a.setValue(30)
self.b = QComboBox(self)
self.b.addItems(self.choices)
self.c= QDialogButtonBox(self)
self.c.setStandardButtons(QDialogButtonBox.Cancel|QDialogButtonBox.Ok)
f.addRow("window:" ,self.a)
f.addRow("method:", self.b)
f.addRow("", self.c)
self.connect(self.c, SIGNAL("accepted()"), self.sendData)
self.connect(self.c, SIGNAL("rejected()"), self.reinitialize)
def sendData(self):
self.parent().window = self.a.value()
self.parent().method = self.b.currentText()
self.close()
def reinitialize(self):
self.parent().window = None
self.parent().method = None
self.close()
Dial(self).exec_()
if self.window and self.method:
for spl in self.drawnItems.keys():
if action.text() == spl.shortName():
self.drawnItems[spl].updateData(
MSAbstractTypes.averageSmoothing(self.drawnItems[spl].getData()[1],self.window , self.method),
self.drawnItems[spl].getData()[0])
@pyqtSlot()
def plotEIC(self):
if self.flags == 'spectra':
#show double combobox
#select the good spectra then draw
pass
else:
mass, ok = QInputDialog.getText(self.view, "EIC query", "mass:")
if not (mass and ok):
return
xmlfile = self.fullXmlPath(self.selection[0].data().toString())
if not xmlfile:
xmlfile = self.fullXmlPath(self.selection[0].parent().data().toString())
if not xmlfile:
print "item clicked not recognized..."
return
sample = self.model.sample(xmlfile)
if sample.kind =='HighRes':
error=(sample.ppm/1e6)*float(mass)
x, y = massExtraction(sample, float(mass), error)
from core.MetObjects import MSChromatogram
chrom = MSChromatogram(x_data=x, y_data=y, sample=sample)
else:
chrom = sample.getChromWithTrans(math.ceil(float(mass)))
self.view.addMdiSubWindow(MSQtCanvas([chrom], "EIC %s"%str(mass),
labels={'bottom':'RT(s)', 'left':'INTENSITY'}))
#===========================================================================
# annotate stuff
#===========================================================================
@pyqtSlot()
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 removeAllAnnot(self):
if not self.trashItems:
self.view.showErrorMessage("Error", "No annotation detected")
return
for i in self.trashItems:
self.pw.removeItem(i)
def removeLastAnnot(self):
if not self.trashItems:
self.view.showErrorMessage("Error", "No annotation detected")
self.pw.removeItem(self.trashItems[-1])
