def main():
# synthetic data
from silx.math.fit.functions import sum_gauss
x = numpy.arange(5000)
# (height1, center1, fwhm1, ...) 5 peaks
params1 = (50, 500, 100,
20, 2000, 200,
50, 2250, 100,
40, 3000, 75,
23, 4000, 150)
y0 = sum_gauss(x, *params1)
# random values between [-1;1]
noise = 2 * numpy.random.random(5000) - 1
# make it +- 5%
noise *= 0.05
# 2 gaussians with very large fwhm, as background signal
actual_bg = sum_gauss(x, 15, 3500, 3000, 5, 1000, 1500)
# Add 5% random noise to gaussians and add background
y = y0 + numpy.average(y0) * noise + actual_bg
# Open widget
a = qt.QApplication(sys.argv)
a.lastWindowClosed.connect(a.quit)
def mySlot(ddict):
print(ddict)
w = BackgroundDialog()
w.parametersWidget.parametersWidget.sigBackgroundParamWidgetSignal.connect(mySlot)
w.setData(x, y)
w.exec()
def test(withGUI=True, withTestData=True):
myapp.make_pipeline(withGUI)
if withTestData:
myapp.load_test_data()
if withGUI:
node0 = list(csi.nodes.values())[0]
node0.fileNameFilters = ['*.fio', '*.h5', '*.dat']
from silx.gui import qt
from parseq.gui.mainWindow import MainWindowParSeq
app = qt.QApplication(sys.argv)
mainWindow = MainWindowParSeq()
mainWindow.dataChanged()
mainWindow.show()
node0.widget.tree.setFocus() # important
node0.widget.tree.setCurrentIndex(csi.model.index(0))
from modeltest import ModelTest
node0.widget.files.ModelTest = ModelTest
app.exec_()
else:
import matplotlib.pyplot as plt
for data in csi.dataRootItem.get_items():
plt.plot(data.r, data.ft)
plt.show()
def test():
myapp.make_pipeline(True)
app = qt.QApplication(sys.argv)
mainWindow = AboutDialog(None)
mainWindow.show()
app.exec_()
def example_image(mode):
"""set up the roi stats example for images"""
app = qt.QApplication([])
rectangle_roi, polygon_roi, arc_roi = get_2D_rois()
window = _RoiStatsDisplayExWindow()
window.setRois(rois2D=(rectangle_roi, polygon_roi, arc_roi))
# Create the thread that calls submitToQtMainThread
updateThread = UpdateThread(window.plot)
updateThread.start() # Start updating the plot
# define some image and curve
window.plot.addImage(numpy.arange(10000).reshape(100, 100), legend='img1')
window.plot.addImage(numpy.random.random(10000).reshape(100, 100),
legend='img2',
origin=(0, 100))
window.setStats(STATS)
# add some couple (plotItem, roi) to be displayed by default
img1_item = window.plot.getImage('img1')
img2_item = window.plot.getImage('img2')
window.addItem(item=img2_item, roi=rectangle_roi)
window.addItem(item=img1_item, roi=polygon_roi)
window.addItem(item=img1_item, roi=arc_roi)
window.setUpdateMode(mode)
window.show()
app.exec()
updateThread.stop() # Stop updating the plot
def main():
app = qt.QApplication([])
## load data from data/lena.hdf5
datapath = 'data/lena.hdf5'
f = h5py.File(datapath)
image = numpy.array(f['lena'], dtype='float32')
showH5ls(datapath)
plotimage = plotHistogram(image)
# create a PlotAction which plot the histogram for the current image
#
# - using silx.gui.plot.PlotActions.PlotAction
#
# - doc@ http://www.silx.org/doc/silx/dev/modules/gui/plot/actions/examples.html
#
myaction = ComputeHistogramAction(image)
## Add this action into the toolBar of the window
# TODO ...
toolBar = plotimage.toolBar()
# TODO ...
# show automatically the histogram when the image change
#
# - using plotImage.sigActiveImageChanged.connect(plotHisto)
# TODO ...
plotimage.show()
app.exec_()
def main(argv=None):
"""Display an image from a file in an :class:`ImageView` widget.
:param argv: list of command line arguments or None (the default)
to use sys.argv.
:type argv: list of str
:return: Exit status code
:rtype: int
:raises IOError: if no image can be loaded from the file
"""
import argparse
import os.path
global app # QApplication must be global to avoid seg fault on quit
app = qt.QApplication([])
sys.excepthook = qt.exceptionHandler
mainWindow = ScatterView()
mainWindow.setAttribute(qt.Qt.WA_DeleteOnClose)
xx, yy, value = createData()
mainWindow.setData(x=xx, y=yy, value=value)
mainWindow.show()
mainWindow.setFocus(qt.Qt.OtherFocusReason)
return app.exec_()
def example_curve(mode):
"""set up the roi stats example for curves"""
app = qt.QApplication([])
roi_1, roi_2 = get_1D_rois()
window = _RoiStatsDisplayExWindow()
window.setRois(rois1D=(roi_2, roi_1))
# define some image and curve
window.plot.addCurve(x=numpy.linspace(0, 10, 56),
y=numpy.arange(56),
legend='curve1',
color='blue')
window.plot.addCurve(x=numpy.linspace(0, 10, 56),
y=numpy.random.random_sample(size=56),
legend='curve2',
color='red')
window.setStats(STATS)
# add some couple (plotItem, roi) to be displayed by default
curve1_item = window.plot.getCurve('curve1')
window.addItem(item=curve1_item, roi=roi_1)
window.addItem(item=curve1_item, roi=roi_2)
curve2_item = window.plot.getCurve('curve2')
window.addItem(item=curve2_item, roi=roi_2)
window.setUpdateMode(mode)
window.show()
app.exec()
def plot_stack(mystack,what="intensity",title0="X",title1="Y",title2="Z"):
from silx.gui.plot.StackView import StackViewMainWindow
from silx.gui import qt
app = qt.QApplication(sys.argv[1:])
sv = StackViewMainWindow()
sv.setColormap("jet", autoscale=True)
if what == "intensity":
sv.setStack(numpy.absolute(mystack))
elif what == "real":
sv.setStack(numpy.real(mystack))
elif what == "imaginary":
sv.setStack(numpy.imag(mystack))
elif what == "phase":
sv.setStack(numpy.angle(mystack))
elif what == "phase_deg":
sv.setStack(numpy.angle(mystack,deg=True))
else:
raise Exception("Undefined label "+what)
sv.setLabels([title0,title1,title2])
sv.show()
app.exec_()
def test_Spectrum(withGUI): # with convenience functions
import parseq_XES_scan as myapp
myapp.make_pipeline(withGUI)
myapp.load_test_data()
if withGUI:
from silx.gui import qt
from parseq.gui.dataTreeModelView import DataTreeView
MyTreeView = DataTreeView
app = qt.QApplication(sys.argv)
node = list(csi.nodes.values())[-1]
view1 = MyTreeView(node)
if "qt5" in qt.BINDING.lower():
from modeltest import ModelTest
ModelTest(csi.model, view1)
view1.setWindowTitle("Spectra Tree Model")
# select the 1st item (it is a group)
view1.setCurrentIndex(csi.model.index(0))
view1.show()
app.exec_()
def main():
app = qt.QApplication([])
plot = Plot1D()
x = numpy.arange(21)
y = numpy.arange(21)
plot.addCurve(x=x, y=y, legend='myCurve')
plot.addCurve(x=x, y=(y + 5), legend='myCurve2')
plot.setActiveCurve('myCurve')
plot.addScatter(x=[0, 2, 5, 5, 12, 20],
y=[2, 3, 4, 20, 15, 6],
value=[5, 6, 7, 10, 90, 20],
legend='myScatter')
stats = [
('sum', numpy.sum),
Integral(),
(COM(), '{0:.2f}'),
]
plot.getStatsWidget().setStats(stats)
plot.getStatsWidget().parent().setVisible(True)
plot.show()
app.exec_()
def main(filenames):
app = qt.QApplication([])
viewer = Viewer()
for filename in filenames:
viewer.appendFile(filename)
viewer.setVisible(True)
app.exec_()
def main():
global app
app = qt.QApplication([])
# Create the ad hoc window containing a PlotWidget and associated tools
window = PlotAreaMainWindow(app)
window.setAttribute(qt.Qt.WA_DeleteOnClose)
window.setWindowTitle("PlotArea Main Window")
window.show()
# Add two plot windows to the plot area.
window.plotArea.addPlotWindow(plotType='1D')
window.plotArea.addPlotWindow(plotType='2D')
plot0 = window.plotArea.getPlotWindow(0)
plot1 = window.plotArea.getPlotWindow(1)
# Add an 1D data + 2D image to the plots
x0 = np.linspace(-10, 10, 200)
x1 = np.linspace(-10, 5, 150)
x = np.outer(x0, x1)
image = np.sin(x) / x
plot0.addCurve(x0, np.sin(x0) / x0, legend='test curve 0')
plot0.addCurve(x1, np.sin(x1) / x1 + 0.1, legend='test curve 1')
plot1.addImage(image)
app.exec_()
def main(argv):
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'--backend',
dest="backend",
action="store",
default=None,
help='Set plot backend. Should be "matplotlib" (default) or "opengl"')
options = parser.parse_args(argv[1:])
assert options.backend in (None, 'matplotlib', 'opengl')
qapp = qt.QApplication([])
plot_std = get_plot_std(backend=options.backend)
plot_std.show()
plot_mean = get_plot_mean_baseline(backend=options.backend)
plot_mean.show()
plot_stacked_histo = get_plot_stacked_histogram(backend=options.backend)
plot_stacked_histo.show()
plot_log = get_plot_log(backend=options.backend)
plot_log.show()
qapp.exec()
def makescreenshot(script_or_module, filename):
_logger.info('generate screenshot for %s from %s, binding is %s'
'' % (filename, script_or_module, qt.BINDING))
# Probe Qt binding
if qt.BINDING == 'PyQt4':
def grabWindow(winID):
return qt.QPixmap.grabWindow(winID)
elif qt.BINDING in ('PyQt5', 'PySide2'):
def grabWindow(winID):
screen = qt.QApplication.primaryScreen()
return screen.grabWindow(winID)
global _count
_count = 15
global _TIMEOUT
_TIMEOUT = 1000. # in ms
app = qt.QApplication.instance() or qt.QApplication([])
_logger.debug('Using Qt bindings: %s', qt)
def _grabActiveWindowAndClose():
global _count
activeWindow = qt.QApplication.activeWindow()
if activeWindow is not None:
if activeWindow.isVisible():
# hot fix since issue with pySide2 API
if qt.BINDING == 'PySide2':
pixmap = activeWindow.grab()
else:
pixmap = grabWindow(activeWindow.winId())
saveOK = pixmap.save(filename)
if not saveOK:
_logger.error('Cannot save snapshot to %s', filename)
else:
_logger.error('activeWindow is not visible.')
app.quit()
else:
_count -= 1
if _count > 0:
# Only restart a timer if everything is OK
qt.QTimer.singleShot(_TIMEOUT, _grabActiveWindowAndClose)
else:
app.quit()
raise TimeoutError(
'Aborted: It took too long to have an active window.')
script_or_module = os.path.abspath(script_or_module)
sys.argv = [script_or_module]
sys.path.append(os.path.abspath(os.path.dirname(script_or_module)))
qt.QTimer.singleShot(_TIMEOUT, _grabActiveWindowAndClose)
if sys.version_info < (3, ):
execfile(script_or_module)
else:
with open(script_or_module) as f:
code = compile(f.read(), script_or_module, 'exec')
exec(code, globals(), locals())
def test():
from silx.math.fit import fittheories
from silx.math.fit import fitmanager
from silx.math.fit import functions
from silx.gui.plot.PlotWindow import PlotWindow
import numpy
a = qt.QApplication([])
x = numpy.arange(1000)
y1 = functions.sum_gauss(x, 100, 400, 100)
fit = fitmanager.FitManager(x=x, y=y1)
fitfuns = fittheories.FitTheories()
fit.addtheory(name="Gaussian",
function=functions.sum_gauss,
parameters=("height", "peak center", "fwhm"),
estimate=fitfuns.estimate_height_position_fwhm)
fit.settheory('Gaussian')
fit.configure(
PositiveFwhmFlag=True,
PositiveHeightAreaFlag=True,
AutoFwhm=True,
)
# Fit
fit.estimate()
fit.runfit()
w = ParametersTab()
w.show()
w.fillFromFit(fit.fit_results, view='Gaussians')
y2 = functions.sum_splitgauss(x, 100, 400, 100, 40, 10, 600, 50, 500, 80,
850, 10, 50)
fit.setdata(x=x, y=y2)
# Define new theory
fit.addtheory(name="Asymetric gaussian",
function=functions.sum_splitgauss,
parameters=("height", "peak center", "left fwhm",
"right fwhm"),
estimate=fitfuns.estimate_splitgauss)
fit.settheory('Asymetric gaussian')
# Fit
fit.estimate()
fit.runfit()
w.fillFromFit(fit.fit_results, view='Asymetric gaussians')
# Plot
pw = PlotWindow(control=True)
pw.addCurve(x, y1, "Gaussians")
pw.addCurve(x, y2, "Asymetric gaussians")
pw.show()
a.exec_()
def main():
app = qt.QApplication([])
# Create the ad hoc plot widget and change its default colormap
example = ColormapDialogExample()
example.show()
app.exec_()
def setUpClass(cls):
"""Makes sure Qt is inited"""
cls._oldExceptionHook = sys.excepthook
sys.excepthook = cls.exceptionHandler
# Makes sure a QApplication exists and do it once for all
if not qt.QApplication.instance():
cls._qapp = qt.QApplication([])
def main():
sys.excepthook = logUncaughtExceptions
app = qt.QApplication([])
pyFAI.resources.silx_integration()
widget = CalibrationWindow()
setup(widget.model())
widget.setVisible(True)
app.exec_()
def fitgui(
self,
ylog=False,
legend="data",
loadfromfit=False,
concentrations=True,
spectra=True,
environ_elements=None,
):
if self.app is None:
self.app = qt.QApplication([])
w = McaAdvancedFit.McaAdvancedFit()
# Copy mcafit
x = self.mcafit.xdata0
y = self.mcafit.ydata0
w.setData(x, y, legend=legend, xmin=0, xmax=len(y) - 1)
w.mcafit.configure(self.mcafit.getConfiguration())
# GUI for fitting
if ylog:
w.graphWindow.yLogButton.click()
w.graphWindow.energyButton.click()
# w.graphWindow.setGraphYLimits(min(y[y>0]),None)
w.refreshWidgets()
w.show()
result = self.app.exec_()
# Parse result
result = {}
try:
digestedresult = w.mcafit.digestresult()
except AttributeError:
digestedresult = None
if digestedresult:
# Load parameters from fit (if you did "load from fit")
self.miscfromfitresult(digestedresult, out=result)
if concentrations:
self.concentrationsfromfitresult(digestedresult, out=result)
if spectra:
self.spectrafromfitresult(digestedresult, out=result)
if loadfromfit:
config = w.mcafit.getConfiguration()
if concentrations:
self.configadjustconcentrations(config,
result["lmassfractions"],
exclude=environ_elements)
self.loadfrompymca(config=config)
else:
if concentrations or spectra:
result = self.fit(
loadfromfit=loadfromfit,
concentrations=concentrations,
spectra=spectra,
)
return result
def test():
myapp.make_pipeline(withGUI=True)
myapp.load_test_data()
app = qt.QApplication(sys.argv)
mainWindow = CombineSpectraWidget()
mainWindow.setWindowTitle("Combine")
mainWindow.show()
app.exec_()
def test():
myapp.make_pipeline(withGUI=True)
app = qt.QApplication(sys.argv)
dlg = SaveProjectDlg()
dlg.ready.connect(showRes)
dlg.open()
app.exec_()
def main():
global app
app = qt.QApplication([])
# Create the ad hoc window containing a PlotWidget and associated tools
window = MyPlotWindow()
window.setAttribute(qt.Qt.WA_DeleteOnClose)
window.show()
window.showImage()
app.exec_()
def main():
app = qt.QApplication([])
sys.excepthook = qt.exceptionHandler
window = FindContours()
window.generateIsland()
window.show()
result = app.exec()
# remove ending warnings relative to QTimer
app.deleteLater()
return result
def main():
app = qt.QApplication([])
widget = DataViewerFrame()
widget.addView(MyColorView(widget))
widget.setData(Color.GREEN)
widget.show()
result = app.exec()
# remove ending warnings relative to QTimer
app.deleteLater()
sys.exit(result)
def setUpClass(cls):
cls.app = None
if sys.platform.startswith('linux') and not os.environ.get(
'DISPLAY', ''):
# On linux and no DISPLAY available (e.g., ssh without -X)
logger.warning(
'pyFAI.integrate_widget tests disabled (DISPLAY env. variable not set)'
)
cls.app = None
elif qt is not None:
cls.app = qt.QApplication([])
def create_plot2d():
from silx.gui.plot import Plot2D
global app # QApplication must be global to avoid seg fault on quit
app = qt.QApplication([])
plot = Plot2D() # Create the plot widget
plot.setAttribute(qt.Qt.WA_DeleteOnClose)
plot.setKeepDataAspectRatio(
False) # To keep aspect ratio between X and Y axes
plot.show() # Make the plot widget visible
plot.setFocus(qt.Qt.OtherFocusReason)
return plot
def main(filenames):
app = qt.QApplication([])
tree = hdf5.Hdf5TreeView()
tree.setVisible(True)
model = tree.findHdf5TreeModel()
for filename in filenames:
model.insertFile(filename)
app.exec_()
def main(filenames):
"""
:param filenames: list of file paths
"""
app = qt.QApplication([])
sys.excepthook = qt.exceptionHandler
window = Hdf5TreeViewExample(filenames)
window.show()
result = app.exec_()
# remove ending warnings relative to QTimer
app.deleteLater()
sys.exit(result)
def setUpClass(cls):
cls.app = None
if sys.platform.startswith('linux') and not os.environ.get('DISPLAY', ''):
# On linux and no DISPLAY available (e.g., ssh without -X)
logger.warning('pyFAI.integrate_widget tests disabled (DISPLAY env. variable not set)')
cls.app = None
elif qt is not None:
cls.app = qt.QApplication([])
config = {"poni": UtilsTest.getimage("Pilatus1M.poni")}
integration_config.normalize(config, inplace=True)
cls.base_config = config
def qapp(use_gui, xvfb, request):
_set_qt_binding(request.config.option.qt_binding)
from silx.gui import qt
app = qt.QApplication.instance()
if app is None:
app = qt.QApplication([])
try:
yield app
finally:
if app is not None:
app.closeAllWindows()
