[orange-add on] integrate the XasObjectViewer in the pymca orange add-on

orangecontrib/xas/widgets/exafs.py

@@ -29,40 +29,104 @@ __date__ = "06/07/2019"
 
 
 from silx.gui import qt
-from silx.gui.plot import Plot1D, LegendSelector
+from silx.gui.plot import LegendSelector
 from Orange.widgets import gui
 from Orange.widgets.widget import OWWidget
-from xas.core.types import XASObject
-from PyMca5.PyMcaGui.physics.xas.XASPostEdgeParameters import XASPostEdgeParameters
 from Orange.widgets.settings import Setting
+from xas.core.types import XASObject, Spectrum
 import xas.core.process.exafs
+from xas.gui.XasObjectViewer import XasObjectViewer, _CurveOperation, ViewType
+from PyMca5.PyMcaGui.physics.xas.XASPostEdgeParameters import XASPostEdgeParameters
 import logging
 
 _logger = logging.getLogger(__file__)
 
 
+def _exafs_signal_plot(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    missing_keys = spectrum.get_missing_keys(('EXAFSKValues', 'EXAFSSignal'))
+    if missing_keys:
+        _logger.error('missing keys:', missing_keys, 'unable to compute exafs signal plot')
+        return
+    k = spectrum["EXAFSKValues"]
+    if "KMin" not in spectrum:
+        spectrum["KMin"] = k.min()
+    if "KMax" not in spectrum:
+        spectrum["KMax"] = k.max()
+
+    idx = (spectrum["EXAFSKValues"] >= spectrum["KMin"]) & \
+          (spectrum["EXAFSKValues"] <= spectrum["KMax"])
+    x = spectrum["EXAFSKValues"][idx]
+    y = spectrum["EXAFSSignal"][idx]
+    return _CurveOperation(x=x, y=y, legend="EXAFSSignal")
+
+
+def _exafs_postedge_plot(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    missing_keys = spectrum.get_missing_keys(('EXAFSKValues', 'PostEdgeB'))
+    if missing_keys:
+        _logger.error('missing keys:', missing_keys, 'unable to compute exafs postedge plot')
+        return
+    k = spectrum["EXAFSKValues"]
+    if "KMin" not in spectrum:
+        spectrum["KMin"] = k.min()
+    if "KMax" not in spectrum:
+        spectrum["KMax"] = k.max()
+
+    idx = (spectrum["EXAFSKValues"] >= spectrum["KMin"]) & \
+          (spectrum["EXAFSKValues"] <= spectrum["KMax"])
+
+    x = spectrum["EXAFSKValues"][idx]
+    y = spectrum["PostEdgeB"][idx]
+    return _CurveOperation(x=x, y=y, legend="PostEdge")
+
+
+def _exafs_knots_plot(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    missing_keys = spectrum.get_missing_keys(('KnotsX', 'KnotsY'))
+    if missing_keys:
+        _logger.error('missing keys:', missing_keys, 'unable to compute exafs knot plot')
+        return
+    x = spectrum["KnotsX"]
+    y = spectrum["KnotsY"]
+    return _CurveOperation(x=x, y=y, legend="Knots", linestyle="", symbol="o")
+
+
 class ExafsWindow(qt.QMainWindow):
     def __init__(self, parent=None):
         qt.QMainWindow.__init__(self, parent)
-        self.plot = Plot1D()
-        self.setCentralWidget(self.plot)
+        self.xasObjViewer = XasObjectViewer()
+        self.xasObjViewer._spectrumView._plot.getXAxis().setLabel("K")
+        self.xasObjViewer._spectrumView._plot.getYAxis().setLabel("Normalized Units")
+        self.setCentralWidget(self.xasObjViewer)
+
+        # pymca window
         self._pymcaWindow = XASPostEdgeParameters(parent=self)
         dockWidget = qt.QDockWidget(parent=self)
-
         dockWidget.setWidget(self._pymcaWindow)
         self.addDockWidget(qt.Qt.RightDockWidgetArea, dockWidget)
         dockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
         dockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
         self.setWindowFlags(qt.Qt.Widget)
-        # legend
+
+        # legend selector
         self.legendDockWidget = LegendSelector.LegendsDockWidget(parent=self,
-                                                                 plot=self.plot)
+                                                                 plot=self.xasObjViewer._spectrumView._plot)
         self.legendDockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
         self.legendDockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
         self.addDockWidget(qt.Qt.RightDockWidgetArea, self.legendDockWidget)
 
+        self.setWindowFlags(qt.Qt.Widget)
+
+        # plot settings
+        for ope in (_exafs_signal_plot, _exafs_postedge_plot, _exafs_knots_plot,):
+            self.xasObjViewer._spectrumView.addCurveOperation(ope)
+
     def getNCurves(self):
-        return len(self.plot.getAllCurves())
+        return len(self.xasObjViewer.getAllCurves())
+
+    def _updateLegendView(self):
+        self.legendDockWidget.setVisible(self.xasObjViewer.getViewType() is ViewType.spectrum)
 
 
 class ExafsOW(OWWidget):
@@ -95,8 +159,8 @@ class ExafsOW(OWWidget):
         layout.addWidget(self._window)
         self._latest_xas_obj = None
 
-        self._window.plot.getXAxis().setLabel("K")
-        self._window.plot.getYAxis().setLabel("Normalized Units")
+        self._window.xasObjViewer._spectrumView._plot.getXAxis().setLabel("K")
+        self._window.xasObjViewer._spectrumView._plot.getYAxis().setLabel("Normalized Units")
 
         # manage settings
         if self._pymcaSettings != dict():
@@ -119,40 +183,10 @@ class ExafsOW(OWWidget):
         process_obj = ExafsOW.process_function()
         process_obj.setProperties({'_pymcaSettings': self._window._pymcaWindow.getParameters()})
         xas_obj = process_obj.process(xas_obj)
-        self._updatePlot(xas_obj.spectra)
+        self._window.xasObjViewer.setXASObj(xas_obj)
 
         # emit signal for the plot
         self.send("spectra", xas_obj)
 
-    def _updatePlot(self, ddict):
-        plot = self._window.plot
-        plot.clear()
-
-        k = ddict["EXAFSKValues"]
-        if "KMin" not in ddict:
-            ddict["KMin"] = k.min()
-        if "KMax" not in ddict:
-            ddict["KMax"] = k.max()
-
-        idx = (ddict["EXAFSKValues"] >= ddict["KMin"]) & \
-              (ddict["EXAFSKValues"] <= ddict["KMax"])
-
-        plot.addCurve(x=ddict["EXAFSKValues"][idx],
-                      y=ddict["EXAFSSignal"][idx],
-                      legend="EXAFSSignal",
-                      resetzoom=False)
-
-        plot.addCurve(ddict["EXAFSKValues"][idx],
-                      ddict["PostEdgeB"][idx],
-                      legend="PostEdge",
-                      resetzoom=False)
-
-        plot.addCurve(ddict["KnotsX"],
-                      ddict["KnotsY"],
-                      legend="Knots",
-                      linestyle="",
-                      symbol="o",
-                      resetzoom=True)
-
     def _update_settings(self):
         self._pymcaSettings = self._window._pymcaWindow.getParameters()

orangecontrib/xas/widgets/ft.py

@@ -29,41 +29,77 @@ __date__ = "06/07/2019"
 
 
 from silx.gui import qt
-from silx.gui.plot import Plot1D, LegendSelector
+from silx.gui.plot import LegendSelector
 from Orange.widgets import gui
 from Orange.widgets.widget import OWWidget
 from Orange.widgets.settings import Setting
-from xas.core.types import XASObject
+from xas.core.types import XASObject, Spectrum
 import xas.core.process.ft
+from xas.gui.XasObjectViewer import XasObjectViewer, _CurveOperation, ViewType
 from PyMca5.PyMcaGui.physics.xas.XASFourierTransformParameters import XASFourierTransformParameters
 import logging
 
 _logger = logging.getLogger(__file__)
 
 
+def _ft_intensity_plot(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    missing_keys = spectrum.ft.get_missing_keys(('FTRadius', 'FTIntensity'))
+    if missing_keys:
+        _logger.error('missing keys:', missing_keys, 'unable to compute spectrum plot')
+        return
+    return _CurveOperation(x=spectrum.ft['FTRadius'],
+                           y=spectrum.ft['FTIntensity'],
+                           legend="FT Intensity")
+
+
+def _ft_imaginary_plot(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    missing_keys = spectrum.ft.get_missing_keys(('FTRadius', 'FTImaginary'))
+    if missing_keys:
+        _logger.error('missing keys:', missing_keys, 'unable to compute spectrum plot')
+        return
+    return _CurveOperation(x=spectrum.ft['FTRadius'],
+                           y=spectrum.ft['FTImaginary'],
+                           legend="FT Imaginary",
+                           color="red")
+
+
 class FTWindow(qt.QMainWindow):
     def __init__(self, parent=None):
         qt.QMainWindow.__init__(self, parent)
-        self.plot = Plot1D()
-        self.setCentralWidget(self.plot)
+
+        # xas object viewer
+        self.xasObjViewer = XasObjectViewer()
+        self.xasObjViewer._spectrumView._plot.getXAxis().setLabel("R (Angstrom)")
+        self.xasObjViewer._spectrumView._plot.getYAxis().setLabel("Arbitrary Units")
+        self.setCentralWidget(self.xasObjViewer)
         self._pymcaWindow = XASFourierTransformParameters(parent=self)
         dockWidget = qt.QDockWidget(parent=self)
 
+        # pymca window
         dockWidget.setWidget(self._pymcaWindow)
         self.addDockWidget(qt.Qt.RightDockWidgetArea, dockWidget)
         dockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
         dockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
         self.setWindowFlags(qt.Qt.Widget)
-        # legend
+
+        # legend selector
         self.legendDockWidget = LegendSelector.LegendsDockWidget(parent=self,
-                                                                 plot=self.plot)
+                                                                 plot=self.xasObjViewer._spectrumView._plot)
         self.legendDockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
         self.legendDockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
         self.addDockWidget(qt.Qt.RightDockWidgetArea, self.legendDockWidget)
 
+        # plot settings
+        for ope in (_ft_intensity_plot, _ft_imaginary_plot):
+            self.xasObjViewer._spectrumView.addCurveOperation(ope)
+
     def getNCurves(self):
         return len(self.plot.getAllCurves())
 
+    def _updateLegendView(self):
+        self.legendDockWidget.setVisible(self.xasObjViewer.getViewType() is ViewType.spectrum)
 
 class FTOW(OWWidget):
     """
@@ -95,9 +131,6 @@ class FTOW(OWWidget):
         layout = gui.vBox(self.mainArea, 'fourier transform').layout()
         layout.addWidget(self._window)
 
-        self._window.plot.getXAxis().setLabel("R (Angstrom)")
-        self._window.plot.getYAxis().setLabel("Arbitrary Units")
-
         # manage settings
         if self._pymcaSettings != dict():
             self._window._pymcaWindow.setParameters(self._pymcaSettings)
@@ -119,22 +152,10 @@ class FTOW(OWWidget):
         process_obj.setProperties({'_pymcaSettings': self._window._pymcaWindow.getParameters()})
 
         xas_obj = process_obj.process(xas_obj)
-        self._updatePlot(ddict=xas_obj.spectrum['FT'])
+        self._window.xasObjViewer.setXASObj(xas_obj)
 
         # emit signal for the plot
         self.send("spectra", xas_obj)
 
-    def _updatePlot(self, ddict):
-        self._window.plot.clear()
-        self._window.plot.addCurve(x=ddict["FTRadius"],
-                                   y=ddict["FTIntensity"],
-                                   legend="FT Intensity",)
-
-        self._window.plot.addCurve(x=ddict["FTRadius"],
-                                   y=ddict["FTImaginary"],
-                                   legend="FT Imaginary",
-                                   color="red")
-        self._window.plot.resetZoom()
-
     def _update_settings(self):
         self._pymcaSettings = self._window._pymcaWindow.getParameters()

orangecontrib/xas/widgets/k_weight.py

@@ -28,44 +28,93 @@ __license__ = "MIT"
 __date__ = "06/07/2019"
 
 
-from silx.gui.plot import Plot1D, LegendSelector
+from silx.gui.plot import LegendSelector
 from Orange.widgets import gui
 from Orange.widgets.widget import OWWidget
 from Orange.widgets.settings import Setting
 from silx.gui import qt
-from xas.core.types import XASObject
+from xas.core.types import XASObject, Spectrum
 import xas.core.process.k_weight
+from xas.gui.XasObjectViewer import XasObjectViewer, _CurveOperation
 import logging
 
 _logger = logging.getLogger(__file__)
 
 
+def _normalized_exafs(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    missing_keys = spectrum.get_missing_keys(('EXAFSKValues', 'EXAFSNormalized'))
+    if missing_keys:
+        _logger.error('missing keys:', missing_keys,
+                      'unable to compute normalized EXAFS')
+        return None
+
+    if spectrum["KWeight"]:
+        if spectrum["KWeight"] == 1:
+            ylabel = "EXAFS Signal * k"
+        else:
+            ylabel = "EXAFS Signal * k^%d" % spectrum["KWeight"]
+    else:
+        ylabel = "EXAFS Signal"
+
+    idx = (spectrum["EXAFSKValues"] >= spectrum["KMin"]) & \
+          (spectrum["EXAFSKValues"] <= spectrum["KMax"])
+
+    return _CurveOperation(x=spectrum["EXAFSKValues"][idx],
+                           y=spectrum["EXAFSNormalized"][idx],
+                           legend="Normalized EXAFS",
+                           ylabel=ylabel)
+
+
+def _ft_window_plot(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    missing_keys = spectrum.ft.get_missing_keys(('K', 'WindowWeight'))
+    if missing_keys:
+        _logger.error('missing keys:', missing_keys,
+                      'unable to compute normalized EXAFS')
+        return None
+
+    return _CurveOperation(x=spectrum.ft['K'],
+                           y=spectrum.ft["WindowWeight"],
+                           legend="FT Window",
+                           yaxis="right",
+                           color="red")
+
+
 class KWeightWindow(qt.QMainWindow):
     def __init__(self, parent=None):
         qt.QMainWindow.__init__(self, parent)
-        self.plot = Plot1D()
-        self.setCentralWidget(self.plot)
+        # xas object viewer
+        self.xasObjViewer = XasObjectViewer()
+        self.xasObjViewer._spectrumView._plot.getXAxis().setLabel("K")
+        self.setCentralWidget(self.xasObjViewer)
 
+        # k wright widget
         self._k_widget = qt.QWidget(parent=self)
         self._k_widget.setLayout(qt.QHBoxLayout())
         self._k_widget.layout().addWidget(qt.QLabel('k weight'))
         self._k_spin_box = qt.QSpinBox(parent=self)
         self._k_spin_box.setRange(0, 3)
         self._k_widget.layout().addWidget(self._k_spin_box)
-
         dockWidget = qt.QDockWidget(parent=self)
         dockWidget.setWidget(self._k_widget)
         self.addDockWidget(qt.Qt.RightDockWidgetArea, dockWidget)
         dockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
         dockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
-        self.setWindowFlags(qt.Qt.Widget)
-        # legend
+
+        # legend selector
         self.legendDockWidget = LegendSelector.LegendsDockWidget(parent=self,
-                                                                 plot=self.plot)
+                                                                 plot=self.xasObjViewer._spectrumView._plot)
         self.legendDockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
         self.legendDockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
         self.addDockWidget(qt.Qt.RightDockWidgetArea, self.legendDockWidget)
 
+        self.setWindowFlags(qt.Qt.Widget)
+
+        # plot settings
+        for ope in (_normalized_exafs, _ft_window_plot):
+            self.xasObjViewer._spectrumView.addCurveOperation(ope)
+
     def getNCurves(self):
         return len(self.plot.getAllCurves())
 
@@ -100,8 +149,6 @@ class KWeightOW(OWWidget):
         layout.addWidget(self._window)
         self._latest_xas_obj = None
 
-        self._window.plot.getXAxis().setLabel("K")
-
         # manage settings
         if self._kWeightSetting != 3:
             self._window._k_spin_box.setValue(self._kWeightSetting)
@@ -122,40 +169,10 @@ class KWeightOW(OWWidget):
         process_obj = KWeightOW.process_function()
         process_obj.setProperties({'_kWeightSetting': self._window._k_spin_box.value()})
         xas_obj = process_obj.process(xas_obj)
-        self._updatePlot(xas_obj.spectrum)
+        self._window.xasObjViewer.setXASObj(xas_obj)
 
         # emit signal for the plot
         self.send("spectra", xas_obj)
 
-    def _updatePlot(self, ddict):
-        if ddict is None:
-            return
-        plot = self._window.plot
-
-        if ddict["KWeight"]:
-            if ddict["KWeight"] == 1:
-                ylabel = "EXAFS Signal * k"
-            else:
-                ylabel = "EXAFS Signal * k^%d" % ddict["KWeight"]
-        else:
-            ylabel = "EXAFS Signal"
-        self._window.plot.getYAxis().setLabel(ylabel)
-
-        idx = (ddict["EXAFSKValues"] >= ddict["KMin"]) & \
-              (ddict["EXAFSKValues"] <= ddict["KMax"])
-        plot.addCurve(x=ddict["EXAFSKValues"][idx],
-                      y=ddict["EXAFSNormalized"][idx],
-                      legend="Normalized EXAFS",
-                      ylabel=ylabel,
-                      replace=True)
-
-        plot.addCurve(x=ddict["FT"]["K"],
-                      y=ddict["FT"]["WindowWeight"],
-                      legend="FT Window",
-                      yaxis="right",
-                      color="red",
-                      replace=False)
-        plot.resetZoom()
-
     def _update_settings(self):
         self._kWeightSetting = self._window._k_spin_box.value()

orangecontrib/xas/widgets/normalization.py

@@ -29,24 +29,86 @@ __date__ = "06/07/2019"
 
 
 from silx.gui import qt
-from silx.gui.plot import Plot1D, LegendSelector
+from silx.gui.plot import LegendSelector
 from Orange.widgets import gui
 from Orange.widgets.widget import OWWidget
 from Orange.widgets.settings import Setting
 from PyMca5.PyMcaGui.physics.xas.XASNormalizationParameters import XASNormalizationParameters
 from PyMca5.PyMcaPhysics.xas.XASClass import XASClass
-from xas.core.types import XASObject
+from xas.core.types import XASObject, Spectrum
+from xas.gui.XasObjectViewer import XasObjectViewer, _CurveOperation, ViewType
 import xas.core.process.normalization
 import logging
 
 _logger = logging.getLogger(__file__)
 
 
+def _spectrum_plot(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    missing_keys = spectrum.get_missing_keys(('Edge',))
+    if missing_keys:
+        _logger.error('missing keys:', missing_keys, 'unable to compute spectrum plot')
+        return
+    e0 = spectrum['Edge']
+    x = spectrum.energy - e0
+    y = spectrum.mu
+    return _CurveOperation(x=x, y=y, legend='Spectrum', yaxis=None)
+
+
+def _normalized_spectrum_plot(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    missing_keys = spectrum.get_missing_keys(('Edge', 'NormalizedEnergy',
+                                              'NormalizedPlotMin', 'NormalizedPlotMax',
+                                              'NormalizedMu'))
+    if missing_keys:
+        _logger.error('missing keys:', missing_keys, 'unable to compute normalized spectrum plot')
+        return None
+
+    idx = (spectrum["NormalizedEnergy"] >= spectrum["NormalizedPlotMin"]) & \
+          (spectrum["NormalizedEnergy"] <= spectrum["NormalizedPlotMax"])
+    e0 = spectrum['Edge']
+    x = spectrum["NormalizedEnergy"][idx] - e0
+    y = spectrum["NormalizedMu"][idx]
+    return _CurveOperation(x=x, y=y, legend='Normalized', yaxis='right')
+
+
+def _post_plot(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    missing_keys = spectrum.get_missing_keys(('Edge', 'NormalizedEnergy',
+                                              'NormalizedSignal'))
+    if missing_keys:
+        _logger.error('missing keys:', missing_keys, 'unable to compute post plot')
+        return None
+
+    e0 = spectrum['Edge']
+    x = spectrum['NormalizedEnergy'] - e0
+    y = spectrum["NormalizedSignal"]
+    return _CurveOperation(x=x, y=y, legend='Post', yaxis=None)
+
+
+def _pre_plot(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    missing_keys = spectrum.get_missing_keys(('Edge', 'NormalizedEnergy',
+                                              'NormalizedBackground'))
+    if missing_keys:
+        _logger.error('missing keys:', missing_keys, 'unable to compute pre plot')
+        return None
+
+    e0 = spectrum['Edge']
+    x = spectrum['NormalizedEnergy'] - e0
+    y = spectrum["NormalizedBackground"]
+    return _CurveOperation(x=x, y=y, legend='Pre', yaxis=None)
+
+
 class NormalizationWindow(qt.QMainWindow):
     def __init__(self, parent=None):
         qt.QMainWindow.__init__(self, parent)
-        self.plot = Plot1D()
-        self.setCentralWidget(self.plot)
+
+        # xas object viewer
+        self.xasObjViewer = XasObjectViewer()
+        self.xasObjViewer._spectrumView._plot.getXAxis().setLabel("Energy (eV)")
+        self.xasObjViewer._spectrumView._plot.getYAxis().setLabel("Absorption (a.u.)")
+        self.setCentralWidget(self.xasObjViewer)
         self._pymcaWindow = XASNormalizationParameters(parent=self)
         dockWidget = qt.QDockWidget(parent=self)
 
@@ -56,17 +118,25 @@ class NormalizationWindow(qt.QMainWindow):
         dockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
         dockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
 
-        # legend
+        # legend selector
         self.legendDockWidget = LegendSelector.LegendsDockWidget(parent=self,
-                                                                 plot=self.plot)
+                                                                 plot=self.xasObjViewer._spectrumView._plot)
         self.legendDockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
         self.legendDockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
         self.addDockWidget(qt.Qt.RightDockWidgetArea, self.legendDockWidget)
 
         self.setWindowFlags(qt.Qt.Widget)
 
+        # plot settings
+        for ope in (_spectrum_plot, _normalized_spectrum_plot, _post_plot,
+                    _pre_plot):
+            self.xasObjViewer._spectrumView.addCurveOperation(ope)
+
     def getNCurves(self):
-        return len(self.plot.getAllCurves())
+        return len(self.xasObjViewer._spectrumView._plot.getAllCurves())
+
+    def _updateLegendView(self):
+        self.legendDockWidget.setVisible(self.xasObjViewer.getViewType() is ViewType.spectrum)
 
 
 class NormalizationOW(OWWidget):
@@ -99,9 +169,7 @@ class NormalizationOW(OWWidget):
         self._window = NormalizationWindow(parent=self)
         layout = gui.vBox(self.mainArea, 'fourier transform').layout()
         layout.addWidget(self._window)
-        self._window.plot.setWindowTitle('spectra')
-        self._window.plot.getXAxis().setLabel("Energy (eV)")
-        self._window.plot.getYAxis().setLabel("Absorption (a.u.)")
+        self._window.xasObjViewer.setWindowTitle('spectra')
 
         self.pymca_xas = XASClass()
 
@@ -120,11 +188,13 @@ class NormalizationOW(OWWidget):
         if xas_obj is None:
             return
 
+        # TODO: move process to multiprocessing + add advancement progress
         self._latest_xas_obj = xas_obj.copy()
         process_class = NormalizationOW.process_function()
         process_class.setProperties({'_pymcaSettings': self._window._pymcaWindow.getParameters()})
         xas_obj = process_class(xas_obj)
-        self._updatePlot(xas_obj.spectrum)
+        self._window.xasObjViewer.setXASObj(xas_obj=xas_obj)
+
         # emit signal for the plot
         self.send("spectra", xas_obj)
 
@@ -133,37 +203,5 @@ class NormalizationOW(OWWidget):
         if self._latest_xas_obj:
             self.process(self._latest_xas_obj)
 
-    def _updatePlot(self, ddict):
-        self._window.plot.clear()
-        if ddict is None:
-            return
-        assert isinstance(ddict, dict)
-        idx = (ddict["NormalizedEnergy"] >= ddict["NormalizedPlotMin"]) & \
-                  (ddict["NormalizedEnergy"] <= ddict["NormalizedPlotMax"])
-
-        # first clear connected plot
-        # then create all the requested curve
-        e0 = ddict["Edge"]
-
-        self._window.plot.addCurve(x=ddict["Energy"] - e0,
-                                   y=ddict["Mu"],
-                                   legend="Spectrum")
-
-        self._window.plot.addCurve(x=ddict["NormalizedEnergy"][idx] - e0,
-                                   y=ddict["NormalizedMu"][idx],
-                                   legend="Normalized",
-                                   yaxis='right')
-
-        self._window.plot.addCurve(x=ddict["NormalizedEnergy"] - e0,
-                                   y=ddict["NormalizedSignal"],
-                                   legend="Post",
-                                   resetzoom=False)
-
-        self._window.plot.addCurve(x=ddict["NormalizedEnergy"] - e0,
-                                   y=ddict["NormalizedBackground"],
-                                   legend='Pre',
-                                   resetzoom=False)
-        self._window.plot.resetZoom()
-
     def _update_settings(self):
         self._pymcaSettings = self._window._pymcaWindow.getParameters()

xas/core/types.py

@@ -88,6 +88,8 @@ class XASObject(object):
         assert dim1_idx < self.dim1
         assert dim2_idx < self.dim2
         global_idx = dim1_idx * self.dim2 + dim2_idx
+        assert global_idx < len(self.spectra)
+        assert global_idx >= 0
         return self.spectra[global_idx]
 
     def addSpectrum(self, spectrum):
@@ -221,6 +223,7 @@ class XASObject(object):
 class Spectra(object):
     pass
 
+
 class Spectrum(object):
     _MU_KEY = 'Mu'
 
@@ -387,6 +390,17 @@ class Spectrum(object):
         for key, value in obj.items():
             self[key] = value
 
+    def get_missing_keys(self, keys):
+        """Return missing keys on the spectrum"""
+        missing = []
+        for key in keys:
+            if key not in self:
+                missing.append(key)
+        if len(missing) is 0:
+            return None
+        else:
+            return missing
+
 
 class _FT(object):
 
@@ -460,3 +474,15 @@ class _FT(object):
         }
         res.update(self.__other_parameters)
         return res
+
+    def get_missing_keys(self, keys):
+        """Return missing keys on the spectrum"""
+        missing = []
+        for key in keys:
+            if key not in self:
+                missing.append(key)
+        if len(missing) is 0:
+            return None
+        else:
+            return missing
+

xas/gui/XasObjectViewer.py

@@ -39,6 +39,7 @@ from silx.utils.enum import Enum
 from silx.gui.widgets.FrameBrowser import HorizontalSliderWithBrowser
 from silx.gui import icons as silx_icons
 from silx.gui.colors import Colormap
+from collections import namedtuple
 
 
 class ViewType(Enum):
@@ -140,13 +141,30 @@ class _ExtendedSliderWithBrowser(HorizontalSliderWithBrowser):
         self.layout().insertWidget(0, qt.QLabel(str(name + ':')))
 
 
+class _CurveOperation(object):
+    def __init__(self, x, y, legend, yaxis=None, linestyle=None, symbol=None,
+                 color=None, ylabel=None):
+        self.x = x
+        self.y = y
+        self.legend = legend
+        self.yaxis = yaxis
+        self.linestyle = linestyle
+        self.symbol = symbol
+        self.color = color
+        self.ylabel = ylabel
+
+
 class SpectrumViewer(qt.QMainWindow):
     def __init__(self, parent=None):
+        self._curveOperations = []
+        """List of callaback to produce plot regarding the XASObject.
+        Callback function should return a _curve_operation"""
         qt.QMainWindow.__init__(self, parent)
         self.xas_obj = None
         self._plot = Plot1D(parent=self)
         self.setCentralWidget(self._plot)
 
+        # frame browsers
         dockWidget = qt.QDockWidget(parent=