class ComponentPlotWidget(SpectraPlotWidget):
def __init__(self, *args, **kwargs):
super(ComponentPlotWidget, self).__init__(linePos=800,
txtPosRatio=0.35,
*args,
**kwargs)
self.cross = PlotDataItem([800], [0],
symbolBrush=(255, 255, 255),
symbolPen=(255, 255, 255),
symbol='+',
symbolSize=25)
self._x, self._y = None, None
self.ymax, self.zmax = 0, 100
def getEnergy(self):
if self._y is not None:
x_val = self.line.value()
idx = val2ind(x_val, self._x)
x_val = self._x[idx]
y_val = self._y[idx]
txt_html = f'<div style="text-align: center"><span style="color: #FFF; font-size: 12pt">\
X = {x_val: .2f}, Y = {y_val: .4f}</div>'
self.txt.setHtml(txt_html)
self.cross.setData([x_val], [y_val])
def plot(self, x, y, *args, **kwargs):
# set up infinity line and get its position
plot_item = self.plotItem.plot(x, y, *args, **kwargs)
self.addItem(self.line)
self.addItem(self.cross)
x_val = self.line.value()
idx = val2ind(x_val, x)
x_val = x[idx]
y_val = y[idx]
txt_html = f'<div style="text-align: center"><span style="color: #FFF; font-size: 12pt">\
X = {x_val: .2f}, Y = {y_val: .4f}</div>'
self.txt.setHtml(txt_html)
self.txt.setZValue(self.zmax - 1)
self.cross.setData([x_val], [y_val])
self.cross.setZValue(self.zmax)
ymax = max(y)
if ymax > self.ymax:
self.ymax = ymax
self._x, self._y = x, y
r = self.txtPosRatio
self.txt.setPos(r * x[-1] + (1 - r) * x[0], self.ymax)
self.addItem(self.txt)
return plot_item
class SpectraPlotWidget(PlotWidget):
sigEnergyChanged = Signal(object)
def __init__(self, linePos=650, txtPosRatio=0.35, invertX=True, *args, **kwargs):
"""
A widget to display a 1D spectrum
:param linePos: the initial position of the InfiniteLine
:param txtPosRatio: a coefficient that determines the relative position of the textItem
:param invertX: whether to invert X-axis
"""
super(SpectraPlotWidget, self).__init__(*args, **kwargs)
self._data = None
assert (txtPosRatio >= 0) and (txtPosRatio <= 1), 'Please set txtPosRatio value between 0 and 1.'
self.txtPosRatio = txtPosRatio
self.positionmap = dict()
self.wavenumbers = None
self._meanSpec = True # whether current spectrum is a mean spectrum
self.line = InfiniteLine(movable=True)
self.line.setPen((255, 255, 0, 200))
self.line.setValue(linePos)
self.line.sigPositionChanged.connect(self.sigEnergyChanged)
self.line.sigPositionChanged.connect(self.getEnergy)
self.addItem(self.line)
self.cross = PlotDataItem([linePos], [0], symbolBrush=(255, 0, 0), symbolPen=(255, 0, 0), symbol='+',
symbolSize=20)
self.cross.setZValue(100)
self.addItem(self.cross)
self.txt = TextItem()
self.getViewBox().invertX(invertX)
self.spectrumInd = 0
self.selectedPixels = None
self._y = None
def getEnergy(self, lineobject):
if self._y is not None:
x_val = lineobject.value()
idx = val2ind(x_val, self.wavenumbers)
x_val = self.wavenumbers[idx]
y_val = self._y[idx]
if not self._meanSpec:
txt_html = toHtml(f'Spectrum #{self.spectrumInd}')
else:
txt_html = toHtml(f'{self._mean_title}')
txt_html += toHtml(f'X = {x_val: .2f}, Y = {y_val: .4f}')
self.txt.setHtml(txt_html)
self.cross.setData([x_val], [y_val])
def setHeader(self, header: NonDBHeader, field: str, *args, **kwargs):
self.header = header
self.field = field
# get wavenumbers
spectraEvent = next(header.events(fields=['spectra']))
self.wavenumbers = spectraEvent['wavenumbers']
self.N_w = len(self.wavenumbers)
self.rc2ind = spectraEvent['rc_index']
# make lazy array from document
data = None
try:
data = header.meta_array(field)
except IndexError:
msg.logMessage(f'Header object contained no frames with field {field}.', msg.ERROR)
if data is not None:
# kwargs['transform'] = QTransform(1, 0, 0, -1, 0, data.shape[-2])
self._data = data
def showSpectra(self, i=0):
if (self._data is not None) and (i < len(self._data)):
self.getViewBox().clear()
self._meanSpec = False
self.spectrumInd = i
self.plot(self.wavenumbers, self._data[i])
def getSelectedPixels(self, selectedPixels):
self.selectedPixels = selectedPixels
# print(selectedPixels)
def clearAll(self):
# remove legend
_legend = self.plotItem.legend
if (_legend is not None) and (_legend.scene() is not None):
_legend.scene().removeItem(_legend)
self.getViewBox().clear()
def showMeanSpectra(self):
self._meanSpec = True
self.getViewBox().clear()
if self.selectedPixels is not None:
n_spectra = len(self.selectedPixels)
tmp = np.zeros((n_spectra, self.N_w))
for j in range(n_spectra): # j: jth selected pixel
row_col = tuple(self.selectedPixels[j])
tmp[j, :] = self._data[self.rc2ind[row_col]]
self._mean_title = f'ROI mean of {n_spectra} spectra'
else:
n_spectra = len(self._data)
tmp = np.zeros((n_spectra, self.N_w))
for j in range(n_spectra):
tmp[j, :] = self._data[j]
self._mean_title = f'Total mean of {n_spectra} spectra'
if n_spectra > 0:
meanSpec = np.mean(tmp, axis=0)
else:
meanSpec = np.zeros_like(self.wavenumbers) + 1e-3
self.plot(self.wavenumbers, meanSpec)
def plot(self, x, y, *args, **kwargs):
# set up infinity line and get its position
self.plotItem.plot(x, y, *args, **kwargs)
self.addItem(self.line)
self.addItem(self.cross)
x_val = self.line.value()
if x_val == 0:
y_val = 0
else:
idx = val2ind(x_val, self.wavenumbers)
x_val = self.wavenumbers[idx]
y_val = y[idx]
if not self._meanSpec:
txt_html = toHtml(f'Spectrum #{self.spectrumInd}')
else:
txt_html = toHtml(f'{self._mean_title}')
txt_html += toHtml(f'X = {x_val: .2f}, Y = {y_val: .4f}')
self.txt.setHtml(txt_html)
ymax = np.max(y)
self._y = y
r = self.txtPosRatio
self.txt.setPos(r * x[-1] + (1 - r) * x[0], ymax)
self.cross.setData([x_val], [y_val])
self.addItem(self.txt)
