def _graphSignal(self, ddict, ownsignal = None):
if self.changeTagOn:
if self.__selectionMask is not None and ddict['event']=="mouseClicked" and ddict['button']=="middle" :
x,y = int(ddict["x"]), int(ddict["y"])
y, x = sole_MaskImageWidget.convertToRowAndColumn(x , y,
self.__imageData.shape,
xScale=self._xScale,
yScale=self._yScale,
safe=True)
id_target = self.__selectionMask[y,x]
if id_target and id_target!= self._nRoi:
mask_target = (self.__selectionMask == id_target )
mask_swap = (self.__selectionMask== self._nRoi)
self.__selectionMask [mask_target] = self._nRoi
self.__selectionMask [mask_swap] = id_target
emitsignal = True
if emitsignal:
self.plotImage(update = False)
self._emitMaskChangedSignal()
return
# super(MaskImageWidget, self)._graphSignal(ddict, ownsignal)
sole_MaskImageWidget.MaskImageWidget._graphSignal(self, ddict, ownsignal)
def _rixsID26(self):
allCurves = self.getAllCurves()
nCurves = len(allCurves)
if nCurves < 2:
msg = "ID26 RIXS scans are built combining several single scans"
raise ValueError(msg)
self._xLabel = self.getGraphXLabel()
self._yLabel = self.getGraphYLabel()
if self._xLabel not in [
"energy", "Spec.Energy", "arr_hdh_ene", "Mono.Energy"
]:
msg = "X axis does not correspond to a BM20 or ID26 RIXS scan"
raise ValueError(msg)
motorNames = allCurves[0][3]["MotorNames"]
if self._xLabel == "Spec.Energy":
# ID26
fixedMotorMne = "Mono.Energy"
elif (self._xLabel == "energy") and ("xes_en" in motorNames):
# BM20 case
fixedMotorMne = "xes_en"
elif "Spec.Energy" in motorNames:
# ID26
fixedMotorMne = "Spec.Energy"
else:
# TODO: Show a combobox to allow the selection of the "motor"
msg = "Cannot automatically recognize motor mnemomnic to be used"
raise ValueError(msg)
fixedMotorIndex = allCurves[0][3]["MotorNames"].index(fixedMotorMne)
#get the min and max values of the curves
if fixedMotorMne == "Mono.Energy":
info = allCurves[0][3]
xMin = info["MotorValues"][fixedMotorIndex]
xMax = xMin
nData = 0
i = 0
minValues = numpy.zeros((nCurves, ), numpy.float64)
for curve in allCurves:
info = curve[3]
tmpMin = info['MotorValues'][fixedMotorIndex]
tmpMax = info['MotorValues'][fixedMotorIndex]
minValues[i] = tmpMin
if tmpMin < xMin:
xMin = tmpMin
if tmpMax > xMax:
xMax = tmpMax
nData += len(curve[0])
i += 1
else:
xMin = allCurves[0][0][0] # ID26 data are already ordered
xMax = allCurves[0][0][-1]
minValues = numpy.zeros((nCurves, ), numpy.float64)
minValues[0] = xMin
nData = len(allCurves[0][0])
i = 0
for curve in allCurves[1:]:
i += 1
tmpMin = curve[0][0]
tmpMax = curve[0][-1]
minValues[i] = tmpMin
if tmpMin < xMin:
xMin = tmpMin
if tmpMax > xMax:
xMax = tmpMax
nData += len(curve[0])
#sort the curves
orderIndex = minValues.argsort()
#print "ORDER INDEX = ", orderIndex
# express data in eV
if (xMax - xMin) < 5.0:
# it seems data need to be multiplied
factor = 1000.
else:
factor = 1.0
motor2Values = numpy.zeros((nCurves, ), numpy.float64)
xData = numpy.zeros((nData, ), numpy.float32)
yData = numpy.zeros((nData, ), numpy.float32)
zData = numpy.zeros((nData, ), numpy.float32)
start = 0
for i in range(nCurves):
idx = orderIndex[i]
curve = allCurves[idx]
info = curve[3]
nPoints = max(curve[0].shape)
end = start + nPoints
x = curve[0]
z = curve[1]
x.shape = -1
z.shape = -1
if fixedMotorMne == "Mono.Energy":
xData[
start:end] = info["MotorValues"][fixedMotorIndex] * factor
yData[start:end] = x * factor
else:
xData[start:end] = x * factor
yData[
start:end] = info["MotorValues"][fixedMotorIndex] * factor
zData[start:end] = z
start = end
# construct the grid in steps of eStep eV
eStep = 0.05
n = (xMax - xMin) * (factor / eStep)
grid0 = numpy.linspace(xMin * factor, xMax * factor, n)
grid1 = numpy.linspace(yData.min(), yData.max(), n)
# create the meshgrid
xx, yy = numpy.meshgrid(grid0, grid1)
if 0:
# get the interpolated values
try:
zz = griddata(xData, yData, zData, xx, yy)
except RuntimeError:
zz = griddata(xData, yData, zData, xx, yy, interp='linear')
# show them
if self._rixsWidget is None:
self._rixsWidget = MaskImageWidget.MaskImageWidget(\
imageicons=False,
selection=False,
profileselection=True,
scanwindow=self)
self._rixsWidget.setImageData(zz,
xScale=(xx.min(), xx.max()),
yScale=(yy.min(), yy.max()))
self._rixsWidget.show()
elif 1:
etData = xData - yData
grid3 = numpy.linspace(etData.min(), etData.max(), n)
# create the meshgrid
xx, yy = numpy.meshgrid(grid0, grid3)
# get the interpolated values
try:
zz = griddata(xData, etData, zData, xx, yy)
except RuntimeError:
# Natural neighbor interpolation not always possible
zz = griddata(xData, etData, zData, xx, yy, interp='linear')
if self._rixsWidget is None:
self._rixsWidget = MaskImageWidget.MaskImageWidget(\
imageicons=False,
selection=False,
aspect=True,
profileselection=True,
scanwindow=self)
self._rixsWidget.setLineProjectionMode('X')
#actualMax = zData.max()
#actualMin = zData.min()
#zz = numpy.where(numpy.isfinite(zz), zz, actualMax)
shape = zz.shape
xScale = (xx.min(), (xx.max() - xx.min()) / float(zz.shape[1]))
yScale = (yy.min(), (yy.max() - yy.min()) / float(zz.shape[0]))
self._rixsWidget.setImageData(zz, xScale=xScale, yScale=yScale)
self._rixsWidget.setXLabel("Incident Energy (eV)")
self._rixsWidget.setYLabel("Energy Transfer (eV)")
self._rixsWidget.show()
return
def __init__(self, parent=None, graph=None, bgrx=True, image_shape=None):
qt.QWidget.__init__(self, parent)
self.setWindowTitle("PyMca RGB Correlator")
self.setWindowIcon(
qt.QIcon(qt.QPixmap(RGBCorrelatorGraph.IconDict['gioconda16'])))
self.mainLayout = qt.QVBoxLayout(self)
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(6)
self.splitter = qt.QSplitter(self)
self.splitter.setOrientation(qt.Qt.Horizontal)
self.controller = RGBCorrelatorWidget.RGBCorrelatorWidget(
self.splitter, image_shape=image_shape)
self._y1AxisInverted = False
self._imageBuffer = None
self._matplotlibSaveImage = None
standaloneSaving = True
if graph is None:
if MATPLOTLIB:
standaloneSaving = False
if USE_MASK_WIDGET:
self.graphWidgetContainer = MaskImageWidget.MaskImageWidget(
self.splitter,
selection=True,
imageicons=True,
standalonesave=standaloneSaving,
profileselection=False,
polygon=True)
self.graphWidget = self.graphWidgetContainer.graphWidget
else:
self.graphWidget = RGBCorrelatorGraph.RGBCorrelatorGraph(
self.splitter, standalonesave=standaloneSaving)
if not standaloneSaving:
self.graphWidget.saveToolButton.clicked.connect( \
self._saveToolButtonSignal)
self._saveMenu = qt.QMenu()
self._saveMenu.addAction(QString("Standard"),
self.graphWidget._saveIconSignal)
self._saveMenu.addAction(QString("Matplotlib"),
self._saveMatplotlibImage)
self.graph = self.graphWidget.graph
#add flip Icon
self.graphWidget.hFlipToolButton.clicked.connect( \
self._hFlipIconSignal)
self._handleGraph = True
else:
self.graph = graph
self._handleGraph = False
#self.splitter.setStretchFactor(0,1)
#self.splitter.setStretchFactor(1,1)
self.mainLayout.addWidget(self.splitter)
self.reset = self.controller.reset
self.addImage = self.controller.addImage
self.removeImage = self.controller.removeImage
self.addImageSlot = self.controller.addImageSlot
self.removeImageSlot = self.controller.removeImageSlot
self.replaceImageSlot = self.controller.replaceImageSlot
self.setImageShape = self.controller.setImageShape
self.update = self.controller.update
self.transposeImages = self.controller.transposeImages
self.controller.sigRGBCorrelatorWidgetSignal.connect( \
self.correlatorSignalSlot)
self.controller.sigMaskImageWidgetSignal.connect( \
self.maskImageSlot)
def _energyTransfer(self, mode="energytransfer"):
allCurves = self.getAllCurves()
nCurves = len(allCurves)
if nCurves < 2:
msg = "RIXS scans are built combining several single scans"
raise ValueError(msg)
self._xLabel = self.getGraphXLabel()
self._yLabel = self.getGraphYLabel()
if self._xLabel not in \
["energy", "Energy", "Spec.Energy", "arr_hdh_ene", "Mono.Energy"]:
msg = "X axis does not correspond to a supported RIXS scan"
raise ValueError(msg)
motorNames = allCurves[0][3]["MotorNames"]
CHESS = False
if self._xLabel == "Spec.Energy":
# ID26
fixedMotorMne = "Mono.Energy"
elif (self._xLabel == "Energy") and ("xes_dn_ana" in motorNames):
# CHESS
fixedMotorMne = "xes_dn_ana"
CHESS = True
msg = "Please use CHESS provided plugin. Contact beamline staff"
raise RuntimeError(msg)
elif (self._xLabel == "energy") and ("xes_en" in motorNames):
# BM20 case
fixedMotorMne = "xes_en"
elif "Spec.Energy" in motorNames:
# ID26
fixedMotorMne = "Spec.Energy"
else:
# TODO: Show a combobox to allow the selection of the "motor"
msg = "Cannot automatically recognize motor mnemomnic to be used"
raise ValueError(msg)
fixedMotorIndex = allCurves[0][3]["MotorNames"].index(fixedMotorMne)
#get the min and max values of the curves
if fixedMotorMne != "Mono.Energy":
xMin = allCurves[0][0][0] # ID26 data are already ordered
xMax = allCurves[0][0][-1]
minValues = numpy.zeros((nCurves, ), numpy.float64)
minValues[0] = xMin
nData = len(allCurves[0][0])
i = 0
for curve in allCurves[1:]:
i += 1
tmpMin = curve[0][0]
tmpMax = curve[0][-1]
minValues[i] = tmpMin
if tmpMin < xMin:
xMin = tmpMin
if tmpMax > xMax:
xMax = tmpMax
nData += len(curve[0])
else:
info = allCurves[0][3]
xMin = info["MotorValues"][fixedMotorIndex]
xMax = xMin
nData = 0
i = 0
minValues = numpy.zeros((nCurves, ), numpy.float64)
for curve in allCurves:
info = curve[3]
tmpMin = info['MotorValues'][fixedMotorIndex]
tmpMax = info['MotorValues'][fixedMotorIndex]
minValues[i] = tmpMin
if tmpMin < xMin:
xMin = tmpMin
if tmpMax > xMax:
xMax = tmpMax
nData += len(curve[0])
i += 1
#sort the curves
orderIndex = minValues.argsort()
#print "ORDER INDEX = ", orderIndex
# express data in eV
if (xMax - xMin) < 5.0:
# it seems data need to be multiplied
factor = 1000.
else:
factor = 1.0
motor2Values = numpy.zeros((nCurves, ), numpy.float64)
xData = numpy.zeros((nData, ), numpy.float32)
yData = numpy.zeros((nData, ), numpy.float32)
zData = numpy.zeros((nData, ), numpy.float32)
start = 0
for i in range(nCurves):
idx = orderIndex[i]
curve = allCurves[idx]
info = curve[3]
nPoints = max(curve[0].shape)
end = start + nPoints
x = curve[0]
z = curve[1]
x.shape = -1
z.shape = -1
if fixedMotorMne == "Mono.Energy":
xData[
start:end] = info["MotorValues"][fixedMotorIndex] * factor
yData[start:end] = x * factor
elif CHESS:
xData[start:end] = x * factor
#yData[start:end] = info["MotorValues"][fixedMotorIndex]
thetaDeg = 78.1119 + 0.5 * (
info["MotorValues"][fixedMotorIndex] + 5.25)
yData[start:end] = 12398.4 / (
1.656446 * numpy.sin(numpy.pi * thetaDeg / 180.))
else:
xData[start:end] = x * factor
yData[
start:end] = info["MotorValues"][fixedMotorIndex] * factor
zData[start:end] = z
start = end
# construct the grid in steps of eStep eV
eStep = 0.05
n = (xMax - xMin) * (factor / eStep)
grid0 = numpy.linspace(xMin * factor, xMax * factor, n)
grid1 = numpy.linspace(yData.min(), yData.max(), n)
# create the meshgrid
xx, yy = numpy.meshgrid(grid0, grid1)
if 0:
# get the interpolated values
etData = xData - yData
grid3 = numpy.linspace(etData.min(), etData.max(), n)
xx, yy = numpy.meshgrid(grid0, grid3)
try:
zz = griddata(xData, etData, zData, xx, yy)
except RuntimeError:
zz = griddata(xData, etData, zData, xx, yy, interp='linear')
# show them
if self._rixsWidget is None:
self._rixsWidget = MaskImageWidget.MaskImageWidget(\
imageicons=False,
selection=False,
profileselection=True,
scanwindow=self)
shape = zz.shape
xScale = (xx.min(), (xx.max() - xx.min()) / float(zz.shape[1]))
yScale = (yy.min(), (yy.max() - yy.min()) / float(zz.shape[0]))
self._rixsWidget.setImageData(zz, xScale=xScale, yScale=yScale)
self._rixsWidget.setXLabel("Incident Energy (eV)")
self._rixsWidget.setYLabel("Energy Transfer (eV)")
self._rixsWidget.show()
elif 1:
if mode == "mesh":
etData = yData
else:
etData = xData - yData
grid3 = numpy.linspace(etData.min(), etData.max(), n)
# create the meshgrid
xx, yy = numpy.meshgrid(grid0, grid3)
# get the interpolated values
if GRIDDATA == "matplotlib":
try:
zz = griddata(xData, etData, zData, xx, yy)
except:
# Natural neighbor interpolation not always possible
zz = griddata(xData,
etData,
zData,
xx,
yy,
interp='linear')
elif GRIDDATA == "scipy":
zz = griddata((xData, etData), zData, (xx, yy), method='cubic')
else:
raise RuntimeError("griddata function not available")
if self._rixsWidget is None:
self._rixsWidget = MaskImageWidget.MaskImageWidget(\
imageicons=False,
selection=False,
aspect=True,
profileselection=True,
scanwindow=self)
self._rixsWidget.setLineProjectionMode('X')
#actualMax = zData.max()
#actualMin = zData.min()
#zz = numpy.where(numpy.isfinite(zz), zz, actualMax)
shape = zz.shape
xScale = (xx.min(), (xx.max() - xx.min()) / float(zz.shape[1]))
if mode == "energyout":
yScale = (yy.min() + yData.min(),
(yy.max() - yy.min()) / float(zz.shape[0]))
else:
yScale = (yy.min(), (yy.max() - yy.min()) / float(zz.shape[0]))
self._rixsWidget.setXLabel("Incident Energy (eV)")
if mode == "mesh":
self._rixsWidget.setYLabel("Emitted Energy (eV)")
elif mode == "energyout":
self._rixsWidget.setYLabel("Emitted Energy (eV)")
else:
self._rixsWidget.setYLabel("Energy Transfer (eV)")
self._rixsWidget.setImageData(zz, xScale=xScale, yScale=yScale)
# self._rixsWidget.graph.replot()
self._rixsWidget.show()
self._rixsWidget.raise_()
return
def _convert(self):
x, y, legend, info = self.getActiveCurve()
self._x = x[:]
self._y = y[:]
if 'Header' not in info:
raise ValueError("Active curve does not seem to be a mesh scan")
header = info['Header'][0]
item = header.split()
if item[2] not in ['mesh', 'hklmesh']:
raise ValueError("Active curve does not seem to be a mesh scan")
self._xLabel = self.getGraphXLabel()
self._yLabel = self.getGraphYLabel()
self._motor0Mne = item[3]
self._motor1Mne = item[7]
#print("Scanned motors are %s and %s" % (motor0Mne, motor1Mne))
#Assume an EXACTLY regular mesh for both motors
self._motor0 = numpy.linspace(float(item[4]), float(item[5]),
int(item[6]) + 1)
self._motor1 = numpy.linspace(float(item[8]), float(item[9]),
int(item[10]) + 1)
#Didier's contribution: Try to do something if scan has been interrupted
if y.size < (int(item[6]) + 1) * (int(item[10]) + 1):
_logger.warning("WARNING: Incomplete mesh scan")
self._motor1 = numpy.resize(self._motor1,
(y.size / (int(item[6]) + 1), 1))
y = numpy.resize(y, ((y.size / (int(item[6]) + 1) *
(int(item[6]) + 1)), 1))
try:
if xLabel.upper() == motor0Mne.upper():
self._motor0 = self._x
self._motor0Mne = self._xLabel
elif xLabel.upper() == motor1Mne.upper():
self._motor1 = self._x
self._motor1Mne = self._xLabel
elif xLabel == info['selection']['cntlist'][0]:
self._motor0 = self._x
self._motor0Mne = self._xLabel
elif xLabel == info['selection']['cntlist'][1]:
self._motor1 = self._x
self._motor1Mne = self._xLabel
except:
_logger.debug("XLabel should be one of the scanned motors")
self._legend = legend
self._info = info
yView = y[:]
yView.shape = len(self._motor1), len(self._motor0)
if self.imageWidget is None:
self.imageWidget = MaskImageWidget.MaskImageWidget(\
imageicons=False,
selection=False,
profileselection=True,
scanwindow=self)
deltaX = self._motor0[1] - self._motor0[0]
deltaY = self._motor1[1] - self._motor1[0]
self.imageWidget.setImageData(yView,
xScale=(self._motor0[0], deltaX),
yScale=(self._motor1[0], deltaY))
self.imageWidget.setXLabel(self._motor0Mne)
self.imageWidget.setYLabel(self._motor1Mne)
self.imageWidget.show()
def _build(self, math=True, replace=False, scanwindow=False):
if math:
self._buildMath()
self.graphWidget = MaskImageWidget.MaskImageWidget(
self,
colormap=True,
standalonesave=True,
imageicons=False,
profileselection=True,
selection=False,
scanwindow=scanwindow,
aspect=True)
self.nameBox = qt.QWidget(self)
self.nameBox.mainLayout = qt.QHBoxLayout(self.nameBox)
self.nameLabel = qt.QLabel(self.nameBox)
self.nameLabel.setText("Image Name = ")
#self.nameLabel.setText(qt.QString(qt.QChar(0x3A3)))
self.name = qt.QLineEdit(self.nameBox)
self.nameBox.mainLayout.addWidget(self.nameLabel)
self.nameBox.mainLayout.addWidget(self.name)
# The IMAGE selection
#self.imageButtonBox = qt.QWidget(self)
self.imageButtonBox = self.nameBox
buttonBox = self.imageButtonBox
#self.imageButtonBoxLayout = qt.QHBoxLayout(buttonBox)
self.imageButtonBoxLayout = self.nameBox.mainLayout
self.imageButtonBoxLayout.setContentsMargins(0, 0, 0, 0)
self.imageButtonBoxLayout.setSpacing(0)
self.addImageButton = qt.QPushButton(buttonBox)
icon = qt.QIcon(qt.QPixmap(IconDict["rgb16"]))
self.addImageButton.setIcon(icon)
self.addImageButton.setText("ADD IMAGE")
self.removeImageButton = qt.QPushButton(buttonBox)
self.removeImageButton.setIcon(icon)
self.removeImageButton.setText("REMOVE IMAGE")
self.imageButtonBoxLayout.addWidget(self.addImageButton)
self.imageButtonBoxLayout.addWidget(self.removeImageButton)
if replace:
self.replaceImageButton = qt.QPushButton(buttonBox)
self.replaceImageButton.setIcon(icon)
self.replaceImageButton.setText("REPLACE IMAGE")
self.imageButtonBoxLayout.addWidget(self.replaceImageButton)
#self.mainLayout.addWidget(self.nameBox)
self.mainLayout.addWidget(self.graphWidget)
self.mainLayout.addWidget(buttonBox)
self.addImageButton.clicked[()].connect(self._addImageClicked)
self.removeImageButton.clicked[()].connect(self._removeImageClicked)
if replace:
self.replaceImageButton.clicked[()].connect( \
self._replaceImageClicked)
#it consumes too much CPU, therefore only on click
#self.graphWidget.graph.canvas().setMouseTracking(1)
self.graphWidget.graphWidget.showInfo()
self.graphWidget.graphWidget.graph.sigPlotSignal.connect(\
self._graphSignal)
def _build(self, vertical=False):
box = qt.QSplitter(self)
if vertical:
box.setOrientation(qt.Qt.Vertical)
boxmainlayout = qt.QVBoxLayout(box)
else:
box.setOrientation(qt.Qt.Horizontal)
boxmainlayout = qt.QHBoxLayout(box)
self.stackWindow = qt.QWidget(box)
self.stackWindow.mainLayout = qt.QVBoxLayout(self.stackWindow)
self.stackWindow.mainLayout.setContentsMargins(0, 0, 0, 0)
self.stackWindow.mainLayout.setSpacing(0)
self.stackWidget = MaskImageWidget.MaskImageWidget(
self.stackWindow,
selection=False,
standalonesave=False,
imageicons=False,
aspect=True)
self._stackSaveMenu = qt.QMenu()
if HDF5:
self._stackSaveMenu.addAction(
QString("Save Zoomed Stack Region as Spectra"),
self.saveStackAsNeXusSpectra)
self._stackSaveMenu.addAction(
QString("Save Zoomed Stack Region as Images"),
self.saveStackAsNeXusImages)
self._stackSaveMenu.addAction(
QString("Save Zoomed Stack Region as Compressed Spectra"),
self.saveStackAsNeXusCompressedSpectra)
self._stackSaveMenu.addAction(
QString("Save Zoomed Stack Region as Compressed Images"),
self.saveStackAsNeXusCompressedImages)
self._stackSaveMenu.addAction(
QString("Save Zoomed Stack Region as Float32 Spectra"),
self.saveStackAsFloat32NeXusSpectra)
self._stackSaveMenu.addAction(
QString("Save Zoomed Stack Region as Float64 Spectra"),
self.saveStackAsFloat64NeXusSpectra)
self._stackSaveMenu.addAction(
QString("Save Zoomed Stack Region as Float32 Images"),
self.saveStackAsFloat32NeXusImages)
self._stackSaveMenu.addAction(
QString("Save Zoomed Stack Region as Float64 Images"),
self.saveStackAsFloat64NeXusImages)
self._stackSaveMenu.addAction(
QString("Save Zoomed Stack Region as HDF5 /data"),
self.saveStackAsSimplestHDF5)
self._stackSaveMenu.addAction(
QString("Save Zoomed Stack Region as Monochromatic TIFF Images"),
self.saveStackAsMonochromaticTiffImages)
self._stackSaveMenu.addAction(
QString("Save Zoomed Stack Region as Float32 TIFF Images"),
self.saveStackAsFloat32TiffImages)
self._stackSaveMenu.addAction(
QString("Standard Graphics"),
self.stackWidget.graphWidget._saveIconSignal)
self.stackWidget.graphWidget.saveToolButton.clicked.connect( \
self._stackSaveToolButtonSignal)
self.stackGraphWidget = self.stackWidget.graphWidget
self.roiWindow = qt.QWidget(box)
self.roiWindow.mainLayout = qt.QVBoxLayout(self.roiWindow)
self.roiWindow.mainLayout.setContentsMargins(0, 0, 0, 0)
self.roiWindow.mainLayout.setSpacing(0)
standaloneSaving = True
self.roiWidget = MaskImageWidget.MaskImageWidget(
parent=self.roiWindow,
rgbwidget=self.rgbWidget,
selection=True,
colormap=True,
imageicons=True,
standalonesave=standaloneSaving,
profileselection=True,
aspect=True)
infotext = 'Toggle background subtraction from current image\n'
infotext += 'subtracting a straight line between the ROI limits.'
self.roiBackgroundIcon = qt.QIcon(qt.QPixmap(IconDict["subtract"]))
self.roiBackgroundButton = self.roiWidget.graphWidget._addToolButton(\
self.roiBackgroundIcon,
self._roiSubtractBackgroundClicked,
infotext,
toggle = True,
state = False,
position = 6)
self.roiGraphWidget = self.roiWidget.graphWidget
self.stackWindow.mainLayout.addWidget(self.stackWidget)
self.roiWindow.mainLayout.addWidget(self.roiWidget)
box.addWidget(self.stackWindow)
box.addWidget(self.roiWindow)
boxmainlayout.addWidget(self.stackWindow)
boxmainlayout.addWidget(self.roiWindow)
self.mainLayout.addWidget(box)
#add some missing icons
offset = 6
infotext = 'If checked, spectra will be added normalized to the number\n'
infotext += 'of pixels. Be carefull if you are preparing a batch and you\n'
infotext += 'fit the normalized spectra because the data in the batch will\n'
infotext += 'have a different weight because they are not normalized.'
self.normalizeIcon = qt.QIcon(qt.QPixmap(IconDict["normalize16"]))
self.normalizeButton = self.stackGraphWidget._addToolButton(\
self.normalizeIcon,
self.normalizeIconChecked,
infotext,
toggle = True,
state = False,
position = 6)
offset += 1
if self.master:
self.loadIcon = qt.QIcon(qt.QPixmap(IconDict["fileopen"]))
self.loadStackButton = self.stackGraphWidget._addToolButton(\
self.loadIcon,
self.loadSlaveStack,
'Load another stack of same shape',
position = offset)
offset += 1
self.pluginIcon = qt.QIcon(qt.QPixmap(IconDict["plugin"]))
infotext = "Call/Load Stack Plugins"
self.stackGraphWidget._addToolButton(self.pluginIcon,
self._pluginClicked,
infotext,
toggle=False,
state=False,
position=offset)
def _convert(self):
x, y, legend, info = self.getActiveCurve()
self._x = x
self._y = y
if 'Header' not in info:
raise ValueError("Active curve does not seem to be a mesh scan")
header = info['Header'][0]
item = header.split()
if item[2] not in ['mesh', 'hklmesh']:
raise ValueError("Active curve does not seem to be a mesh scan")
self._xLabel = self.getGraphXLabel()
self._yLabel = self.getGraphYLabel()
self._motor0Mne = item[3]
self._motor1Mne = item[7]
#print("Scanned motors are %s and %s" % (motor0Mne, motor1Mne))
#Assume an EXACTLY regular mesh for both motors
self._motor0 = numpy.linspace(float(item[4]), float(item[5]),
int(item[6]) + 1)
self._motor1 = numpy.linspace(float(item[8]), float(item[9]),
int(item[10]) + 1)
try:
if xLabel.upper() == motor0Mne.upper():
self._motor0 = self._x
self._motor0Mne = self._xLabel
elif xLabel.upper() == motor1Mne.upper():
self._motor1 = self._x
self._motor1Mne = self._xLabel
elif xLabel == info['selection']['cntlist'][0]:
self._motor0 = self._x
self._motor0Mne = self._xLabel
elif xLabel == info['selection']['cntlist'][1]:
self._motor1 = self._x
self._motor1Mne = self._xLabel
except:
if DEBUG:
print("XLabel should be one of the scanned motors")
self._legend = legend
self._info = info
y.shape = len(self._motor1), len(self._motor0)
if self.imageWidget is None:
self.imageWidget = MaskImageWidget.MaskImageWidget(\
imageicons=False,
selection=False,
profileselection=True,
scanwindow=self)
self.imageWidget.setImageData(y,
xScale=(self._motor0[0],
self._motor0[-1]),
yScale=(self._motor1[0],
self._motor1[-1]))
self.imageWidget.setXLabel(self._motor0Mne)
self.imageWidget.setYLabel(self._motor1Mne)
self.imageWidget.show()
def _convert(self):
x, y, legend, info = self.getActiveCurve()
self._x = x[:]
self._y = y[:]
if 'Header' in info:
# SPEC
command = info['Header'][0]
elif "title" in info:
command = info["title"]
else:
raise ValueError("Active curve does not seem to be a mesh scan")
if "mesh" not in command:
raise ValueError("Active curve does not seem to be a mesh scan")
idx = command.index("mesh")
item = command[idx:].split()
xLabel = self.getGraphXLabel()
yLabel = self.getGraphYLabel()
m0idx = 1
m1idx = 5
self._motor0Mne = item[m0idx]
self._motor1Mne = item[m1idx]
#print("Scanned motors are %s and %s" % (self._motor0Mne, self._motor1Mne))
#print("MOTOR 0 ", float(item[m0idx + 1]),
# float(item[m0idx + 2]),
# int(item[m0idx + 3]))
#print("MOTOR 1 ", float(item[m1idx + 1]),
# float(item[m1idx + 2]),
# int(item[m1idx + 3]))
_logger.info("Assuming scans written in terms of number of intervals")
plusOne = 1
#Assume an EXACTLY regular mesh for both motors
self._motor0 = numpy.linspace(float(item[m0idx + 1]),
float(item[m0idx + 2]),
int(item[m0idx + 3]) + plusOne)
self._motor1 = numpy.linspace(float(item[m1idx + 1]),
float(item[m1idx + 2]),
int(item[m1idx + 3]) + plusOne)
#Didier's contribution: Try to do something if scan has been interrupted
if y.size < (int(item[m0idx + 3]) + plusOne) * (int(item[m1idx + 3]) +
plusOne):
_logger.warning("WARNING: Incomplete mesh scan")
self._motor1 = numpy.resize(
self._motor1, (y.size // (int(item[m0idx + 3]) + plusOne), 1))
y = numpy.resize(y,((y.size // (int(item[m0idx + 3])+plusOne) * \
(int(item[m0idx + 3])+plusOne)),1))
try:
if xLabel.upper() == motor0Mne.upper():
self._motor0 = self._x
self._motor0Mne = self._xLabel
elif xLabel.upper() == motor1Mne.upper():
self._motor1 = self._x
self._motor1Mne = self._xLabel
elif xLabel == info['selection']['cntlist'][0]:
self._motor0 = self._x
self._motor0Mne = self._xLabel
elif xLabel == info['selection']['cntlist'][1]:
self._motor1 = self._x
self._motor1Mne = self._xLabel
except:
_logger.debug("XLabel should be one of the scanned motors")
if "dmesh" in command:
# relative positions, we have to provide an offset
# the offset should be in the positioners if present
offsets = []
if ["MotorNames" in info] and ["MotorValues" in info]:
for key in [self._motor0Mne, self._motor1Mne]:
if key in info["MotorNames"]:
idx = info["MotorNames"].index(key)
offsets.append(info["MotorValues"][idx])
if len(offsets) == 2:
self._motor0 += offsets[0]
self._motor1 += offsets[1]
else:
_logger.warning("Using relative positions")
self._legend = legend
self._info = info
yView = y[:]
yView.shape = len(self._motor1), len(self._motor0)
if self.imageWidget is None:
self.imageWidget = MaskImageWidget.MaskImageWidget(\
imageicons=False,
selection=False,
profileselection=True,
aspect=True,
scanwindow=self)
deltaX = self._motor0[1] - self._motor0[0]
deltaY = self._motor1[1] - self._motor1[0]
self.imageWidget.setImageData(yView,
xScale=(self._motor0[0], deltaX),
yScale=(self._motor1[0], deltaY))
self.imageWidget.setXLabel(self._motor0Mne)
self.imageWidget.setYLabel(self._motor1Mne)
self.imageWidget.show()