def plot(self):
if self.plotDialog is None:
from PyMca5.PyMcaGui.plotting.PlotWindow import PlotWindow
dialog = qt.QDialog(self)
dialog.mainLayout = qt.QVBoxLayout(dialog)
dialog.mainLayout.setContentsMargins(0, 0, 0, 0)
dialog.mainLayout.setSpacing(0)
dialog.plotWidget = PlotWindow(dialog,
newplot=False,
fit=False,
plugins=False,
control=True,
position=True)
dialog.plotWidget.setDefaultPlotLines(True)
dialog.plotWidget.setDefaultPlotPoints(True)
dialog.plotWidget.setDataMargins(0.05, 0.05, 0.05, 0.05)
dialog.mainLayout.addWidget(dialog.plotWidget)
self.plotDialog = dialog
legend = self._transmissionTable["name"]
if legend == "":
legend = None
x = self._transmissionTable["energy"]
y = self._transmissionTable["transmission"]
comment = self._transmissionTable["comment"]
self.plotDialog.plotWidget.addCurve(x,
y,
legend=legend,
xlabel="Energy (keV)",
ylabel="Transmission",
replot=True,
replace=True)
self.plotDialog.plotWidget.setGraphTitle(comment)
def _startThread(self, sthread, message):
sthread.start()
msg = qt.QDialog(self, qt.Qt.FramelessWindowHint)
msg.setModal(1)
msg.setWindowTitle("Please Wait")
layout = qt.QHBoxLayout(msg)
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
l1 = qt.QLabel(msg)
l1.setFixedWidth(l1.fontMetrics().width('##'))
l2 = qt.QLabel(msg)
l2.setText("%s" % message)
l3 = qt.QLabel(msg)
l3.setFixedWidth(l3.fontMetrics().width('##'))
layout.addWidget(l1)
layout.addWidget(l2)
layout.addWidget(l3)
msg.show()
qApp = qt.QApplication.instance()
qApp.processEvents()
i = 0
ticks = ['-', '\\', "|", "/", "-", "\\", '|', '/']
while (sthread.isRunning()):
i = (i + 1) % 8
l1.setText(ticks[i])
l3.setText(" " + ticks[i])
qApp = qt.QApplication.instance()
qApp.processEvents()
time.sleep(2)
msg.close()
result = sthread._result
del sthread
self.raise_()
return result
def getDatasetDialog(filename=None, value=False, message=None):
"""
Simple dialog to select a dataset via a double click on the tree
:param filename: Name of the HDF5 file
:param value: If True returns dataset value instead of just the dataset
"""
if filename is None:
from PyMca5.PyMca import PyMcaFileDialogs
fileTypeList = ['HDF5 Files (*.h5 *.nxs *.hdf)', 'HDF5 Files (*)']
message = "Open HDF5 file"
filenamelist, ffilter = PyMcaFileDialogs.getFileList(
parent=None,
filetypelist=fileTypeList,
message=message,
getfilter=True,
single=True,
currentfilter=None)
if len(filenamelist) < 1:
return None
filename = filenamelist[0]
if message is None:
message = 'Select your item by a double click'
hdf5Dialog = qt.QDialog()
hdf5Dialog.setWindowTitle(message)
hdf5Dialog.mainLayout = qt.QVBoxLayout(hdf5Dialog)
hdf5Dialog.mainLayout.setContentsMargins(0, 0, 0, 0)
hdf5Dialog.mainLayout.setSpacing(0)
fileModel = FileModel()
fileView = HDF5Widget(fileModel)
hdf5File = fileModel.openFile(filename, "r")
def _hdf5WidgetSlot(ddict):
if ddict['event'] == "itemDoubleClicked":
if ddict['type'].lower() in ['dataset']:
hdf5Dialog._hdf5Datatset = ddict['name']
hdf5Dialog.accept()
fileView.sigHDF5WidgetSignal.connect(_hdf5WidgetSlot)
hdf5Dialog.mainLayout.addWidget(fileView)
hdf5Dialog.resize(400, 200)
ret = hdf5Dialog.exec_()
if not ret:
return None
dataset = hdf5Dialog._hdf5Datatset
hdf5Dialog = None
if value:
data = hdf5File[dataset].value
# is it dangerous to close the file?
hdf5File.close()
else:
data = hdf5File[dataset]
return data
def _massAttenuationSlot(self, ddict):
try:
compoundList = ddict['CompoundList']
fractionList = ddict['CompoundFraction']
energy = numpy.arange(1, 100, 0.1)
data = Elements.getMaterialMassAttenuationCoefficients(
compoundList, fractionList, energy)
addButton = False
if self.graph is None:
# probably dead code (ScanWindow.ScanWindow not imported)
self.graphDialog = qt.QDialog(self)
self.graphDialog.mainLayout = qt.QVBoxLayout(self.graphDialog)
self.graphDialog.mainLayout.setContentsMargins(0, 0, 0, 0)
self.graphDialog.mainLayout.setSpacing(0)
#self.graph = ScanWindow.ScanWindow(self.graphDialog)
self.graph = ScanWindow(self.graphDialog)
self.graphDialog.mainLayout.addWidget(self.graph)
self.graph._togglePointsSignal()
self.graph.graph.crossPicker.setEnabled(False)
addButton = True
if addButton:
self._addGraphDialogButton()
self.graph.setGraphTitle(ddict['Comment'])
legend = 'Coherent'
self.graph.addCurve(energy,
numpy.array(data[legend.lower()]),
legend=legend,
xlabel='Energy (keV)',
ylabel='Mass Att. (cm2/g)',
replace=True,
replot=False)
for legend in ['Compton', 'Photo', 'Total']:
self.graph.addCurve(energy,
numpy.array(data[legend.lower()]),
legend=legend,
xlabel='Energy (keV)',
ylabel='Mass Att. (cm2/g)',
replace=False,
replot=False)
self.graph.setActiveCurve(legend + ' ' + 'Mass Att. (cm2/g)')
self.graph.setGraphTitle(ddict['Comment'])
if self.graphDialog is not None:
self.graphDialog.exec()
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setInformativeText(str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec()
def _transmissionSlot(self, ddict):
try:
compoundList = ddict['CompoundList']
fractionList = ddict['CompoundFraction']
density = ddict['Density']
thickness = ddict.get('Thickness', 0.1)
energy = numpy.arange(1, 100, 0.1)
data = Elements.getMaterialTransmission(compoundList,
fractionList,
energy,
density=density,
thickness=thickness,
listoutput=False)
addButton = False
if self.graph is None:
# probably dead code (ScanWindow not imported)
self.graphDialog = qt.QDialog(self)
self.graphDialog.mainLayout = qt.QVBoxLayout(self.graphDialog)
self.graphDialog.mainLayout.setContentsMargins(0, 0, 0, 0)
self.graphDialog.mainLayout.setSpacing(0)
#self.graph = ScanWindow.ScanWindow(self.graphDialog)
self.graph = ScanWindow(self.graphDialog)
self.graphDialog.mainLayout.addWidget(self.graph)
self.graph._togglePointsSignal()
self.graph.graph.crossPicker.setEnabled(False)
addButton = True
if addButton:
self._addGraphDialogButton()
if self.__toolMode:
legend = ddict['Comment']
else:
legend = str(self.matCombo.currentText()) +\
" with density = %f g/cm3" % density +\
" and thickness = %f cm" % thickness
self.graph.addCurve(energy,
data['transmission'],
legend=legend,
xlabel='Energy (keV)',
ylabel='Transmission',
replace=True)
self.graph.setGraphTitle(ddict['Comment'])
if self.graphDialog is not None:
self.graphDialog.exec()
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setInformativeText(str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec()
def _loadIniFromHdf5(self, filename):
self.__hdf5Dialog = qt.QDialog()
self.__hdf5Dialog.setWindowTitle('Select the fit configuration dataset by a double click')
self.__hdf5Dialog.mainLayout = qt.QVBoxLayout(self.__hdf5Dialog)
self.__hdf5Dialog.mainLayout.setContentsMargins(0, 0, 0, 0)
self.__hdf5Dialog.mainLayout.setSpacing(0)
fileModel = HDF5Widget.FileModel()
fileView = HDF5Widget.HDF5Widget(fileModel)
with h5py.File(filename, "r") as hdfFile:
fileModel.appendPhynxFile(hdfFile, weakreference=True)
fileView.sigHDF5WidgetSignal.connect(self._hdf5WidgetSlot)
self.__hdf5Dialog.mainLayout.addWidget(fileView)
self.__hdf5Dialog.resize(400, 200)
ret = self.__hdf5Dialog.exec_()
if ret:
initxt = hdfFile[self.__fitConfigDataset][()]
else:
initxt = None
return initxt
def configureFilter(self):
if self._widget is None:
# construct a widget
msg = qt.QDialog()
msg.setWindowTitle("Deglitch Configuration")
msgLayout = qt.QGridLayout()
buttonLayout = qt.QHBoxLayout()
inpThreshold = qt.QDoubleSpinBox()
inpThreshold.setRange(0.,10.)
inpThreshold.setSingleStep(.1)
inpThreshold.setValue(self.threshold)
inpThreshold.setToolTip('Increase width for broad spikes')
inpWidth = qt.QSpinBox()
inpWidth.setRange(1,101)
inpWidth.setSingleStep(2)
inpWidth.setValue(self.width)
inpWidth.setToolTip('Set low threshold for multiple spikes of different markedness')
labelWidth = qt.QLabel('Width (must be odd)')
labelThreshold = qt.QLabel('Threshold (multiple of deviation)')
buttonOK = qt.QPushButton('Ok')
buttonOK.clicked.connect(msg.accept)
buttonCancel = qt.QPushButton('Cancel')
buttonCancel.clicked.connect(msg.reject)
allActiveBG = qt.QButtonGroup()
buttonAll = qt.QCheckBox('Apply to All')
buttonActive = qt.QCheckBox('Apply to Active')
allActiveBG.addButton(buttonAll, 0)
allActiveBG.addButton(buttonActive, 1)
buttonActive.setChecked(True)
buttonLayout.addWidget(qt.HorizontalSpacer())
buttonLayout.addWidget(buttonOK)
buttonLayout.addWidget(buttonCancel)
msgLayout.addWidget(labelWidth,0,0)
msgLayout.addWidget(inpWidth,0,1)
msgLayout.addWidget(labelThreshold,1,0)
msgLayout.addWidget(inpThreshold,1,1)
msgLayout.addWidget(buttonActive,2,0)
msgLayout.addWidget(buttonAll,2,1)
msgLayout.addLayout(buttonLayout,3,0,1,2)
msg.setLayout(msgLayout)
msg.inputWidth = inpWidth
msg.inputThreshold = inpThreshold
msg.applyToAll = buttonAll
self._widget = msg
self._widget.buttonActive = buttonActive
self._widget.buttonAll = buttonAll
if self._widget.exec():
self.threshold = float(self._widget.inputThreshold.value())
self.width = int(self._widget.inputWidth.value())
if not (self.width%2):
self.width += 1
if self._widget.buttonAll.isChecked():
_logger.debug('AllChecked')
self.removeSpikesAll()
elif self._widget.buttonActive.isChecked():
_logger.debug('ActiveChecked')
self.removeSpikesActive()
def _shiftFromFile(self):
stack = self.getStackDataObject()
if stack is None:
return
data = stack.data
mcaIndex = stack.info.get('McaIndex')
if not (mcaIndex in [0, -1, 2]):
raise IndexError("1D index must be 0, 2, or -1")
filefilter = ['HDF5 Files (*.h5 *.nxs *.hdf *.hdf5)', 'CSV 2-column (*.csv)', 'ASCII 2-column (*)']
filename, ffilter = PyMcaFileDialogs.\
getFileList(parent=None,
filetypelist=filefilter,
message='Load',
mode='OPEN',
single=True,
getfilter=True,
currentfilter=filefilter[0])
if len(filename):
_logger.debug("file name = %s file filter = %s", filename, ffilter)
else:
_logger.debug("nothing selected")
return
filename = filename[0]
if ffilter.startswith('HDF5'):
# browse
self.__hdf5Dialog = qt.QDialog()
self.__hdf5Dialog.setWindowTitle('Select your data set by a double click')
self.__hdf5Dialog.mainLayout = qt.QVBoxLayout(self.__hdf5Dialog)
self.__hdf5Dialog.mainLayout.setContentsMargins(0, 0, 0, 0)
self.__hdf5Dialog.mainLayout.setSpacing(0)
fileModel = HDF5Widget.FileModel()
fileView = HDF5Widget.HDF5Widget(fileModel)
with h5py.File(filename, "r") as hdfFile:
fileModel.appendPhynxFile(hdfFile, weakreference=True)
self.__shiftsDataset = None
fileView.sigHDF5WidgetSignal.connect(self._hdf5WidgetSlot)
self.__hdf5Dialog.mainLayout.addWidget(fileView)
self.__hdf5Dialog.resize(400, 200)
ret = self.__hdf5Dialog.exec_()
if not ret:
return
shifts = hdfFile[self.__shitfsDataset].value
else:
sf = specfilewrapper.Specfile(filename)
nScans = len(sf)
targetScan = None
for scan in sf:
if scan.lines() == data.shape[stack.info['McaIndex']]:
targetScan = scan
break
if targetScan is None:
scan = None
sf = None
raise IOError("Number of read lines does not match stack shape")
shifts = targetScan.data()
targetScan = None
scan = None
sf = None
if shifts.shape[0] == 3 and\
shifts.shape[1] == data.shape[stack.info['McaIndex']]:
# one column was added (point number)
shifts = shifts[1:].T
filename = None
if not isinstance(data, numpy.ndarray):
filefilter = ['HDF5 Files (*.h5)']
filename = PyMcaFileDialogs.\
getFileList(parent=None,
filetypelist=filefilter,
message='Select output file',
mode='SAVE',
single=True,
getfilter=False,
currentfilter=filefilter[0])
if len(filename):
filename = filename[0]
_logger.debug("file name = %s", filename)
else:
raise IOError("No output file selected")
if filename is not None:
self.__hdf5 = self.initializeHDF5File(filename)
crop = False
if _logger.getEffectiveLevel() == logging.DEBUG:
result = self.shiftStack(stack,
shifts,
crop=crop,
filename=filename)
else:
result = self.__shiftStack(stack,
shifts,
crop=crop,
filename=filename)
if result is not None:
# exception occurred
raise Exception(result[1], result[2], result[3])
if filename is not None:
hdf = self.__hdf5
alignmentGroup = hdf['/entry_000/Alignment']
outputShifts = self.getHDF5BufferIntoGroup(alignmentGroup,
shape=(stack.data.shape[mcaIndex], 2),
name="shifts",
dtype=numpy.float32)
outputShifts[:,:] = shifts
attributes={'interpretation':'image'}
# fill the axes information
dataGroup = hdf['/entry_000/Data']
if mcaIndex == 0:
reference_shape = data[0].shape
else:
reference_shape = data.shape[0], data.shape[1]
try:
activeCurve = self.getActiveCurve()
if activeCurve is None:
activeCurve = self.getAllCurves()[0]
x, y, legend, info = activeCurve
dataGroup[info['xlabel']] = numpy.array(x, dtype=numpy.float32)
dataGroup[info['xlabel']].attrs['axis'] = numpy.int32(1)
axesAttribute = '%s:dim_1:dim_2' % info['xlabel']
except:
if _logger.getEffectiveLevel() == logging.DEBUG:
raise
dataGroup['dim_0'] = numpy.arange(stack.data.shape[mcaIndex]).astype(numpy.float32)
dataGroup['dim_0'].attrs['axis'] = numpy.int32(1)
axesAttribute = 'dim_0:dim_1:dim_2'
dataGroup['dim_1'] = numpy.arange(reference_shape[0]).astype(numpy.float32)
dataGroup['dim_1'].attrs['axis'] = numpy.int32(2)
dataGroup['dim_2'] = numpy.arange(reference_shape[1]).astype(numpy.float32)
dataGroup['dim_2'].attrs['axis'] = numpy.int32(3)
dim2 = numpy.arange(reference_shape[1]).astype(numpy.float32)
dataGroup['data'].attrs['axes'] = axesAttribute
self.finishHDF5File(hdf)
else:
self.setStack(stack)
def waitingMessageDialog(thread,
message=None,
parent=None,
modal=True,
update_callback=None,
frameless=False):
"""
thread - The thread to be polled
message - The initial message to be diplayed
parent - The parent QWidget. It is used just to provide a convenient localtion
modal - Default is True. The dialog will prevent user from using other widgets
update_callback - The function to be called to provide progress feedback. It is expected
to return a dictionary. The recognized key words are:
message: The updated message to be displayed.
title: The title of the window title.
progress: A number between 0 and 100 indicating the progress of the task.
status: Status of the calculation thread.
"""
if message is None:
message = "Please wait. Calculation going on."
windowTitle = "Please Wait"
if frameless:
msg = qt.QDialog(None, qt.Qt.FramelessWindowHint)
else:
msg = qt.QDialog(None)
#if modal:
# msg.setWindowFlags(qt.Qt.Window | qt.Qt.CustomizeWindowHint | qt.Qt.WindowTitleHint)
msg.setModal(modal)
msg.setWindowTitle(windowTitle)
layout = qt.QHBoxLayout(msg)
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
l1 = qt.QLabel(msg)
l1.setFixedWidth(l1.fontMetrics().maxWidth() * len('##'))
l2 = qt.QLabel(msg)
l2.setText("%s" % message)
l3 = qt.QLabel(msg)
l3.setFixedWidth(l3.fontMetrics().maxWidth() * len('##'))
layout.addWidget(l1)
layout.addWidget(l2)
layout.addWidget(l3)
msg.show()
if parent is not None:
# place the dialog at appropriate point
parentGeometry = parent.geometry()
x = parentGeometry.x() + 0.5 * parentGeometry.width()
y = parentGeometry.y() + 0.5 * parentGeometry.height()
msg.move(int(x - 0.5 * msg.width()), int(y))
t0 = time.time()
i = 0
ticks = ['-', '\\', "|", "/", "-", "\\", '|', '/']
qApp = qt.QApplication.instance()
if update_callback is None:
while (thread.isRunning()):
i = (i + 1) % 8
l1.setText(ticks[i])
l3.setText(" " + ticks[i])
qApp.processEvents()
if QTHREAD:
qt.QThread.msleep(1000)
else:
time.sleep(2)
else:
while (thread.isRunning()):
updateInfo = update_callback()
message = updateInfo.get('message', message)
windowTitle = updateInfo.get('title', windowTitle)
msg.setWindowTitle(windowTitle)
i = (i + 1) % 8
l1.setText(ticks[i])
l2.setText(message)
l3.setText(" " + ticks[i])
qApp.processEvents()
if QTHREAD:
qt.QThread.msleep(1000)
else:
time.sleep(2)
msg.close()
