[orangecontrib] Add larch orange widgets.

orangecontrib/xas/process.py

@@ -35,7 +35,7 @@ import logging
 _logger = logging.getLogger(__file__)
 
 
-class _PyMcaProcessForOrangeMixIn(object):
+class _ProcessForOrangeMixIn(object):
     """
     Group processing and progress display in a common class for pymca process.
 

orangecontrib/xas/widgets/larch/autobk.py

+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["H. Payno"]
+__license__ = "MIT"
+__date__ = "06/07/2019"
+
+
+import functools
+import logging
+from Orange.widgets import gui
+from Orange.widgets.settings import Setting
+from Orange.widgets.widget import OWWidget
+from silx.gui import qt
+from silx.gui.plot import LegendSelector
+import xas.core.process.larch.autobk
+from orangecontrib.xas.process import _ProcessForOrangeMixIn
+from orangecontrib.xas.process import ProcessRunnable
+from xas.core.types import XASObject, Spectrum
+from xas.gui.XasObjectViewer import XasObjectViewer, _CurveOperation, ViewType
+from xas.gui.larch.autobk import _AutobkParameters
+from orangecontrib.xas.progress import QProgress
+
+_logger = logging.getLogger(__file__)
+
+
+def _plot_bkg(spectrum):
+
+    # bkg = dgroup.bkg
+    # ylabel = plotlabels.mu
+    # if label is None:
+    #     label = 'mu'
+    # #endif
+    # emin, emax = _get_erange(dgroup, emin, emax)
+    # if norm:
+    #     mu  = dgroup.norm
+    #     bkg = (dgroup.bkg - dgroup.pre_edge) / dgroup.edge_step
+    #     ylabel = "%s (norm)" % ylabel
+    #     label = "%s (norm)" % label
+    # #endif
+    # title = _get_title(dgroup, title=title)
+    #
+    # opts = dict(win=win, show_legend=True, linewidth=3,
+    #             delay_draw=True, _larch=_larch)
+    # _plot(dgroup.energy, mu+offset, xlabel=plotlabels.energy, ylabel=ylabel,
+    #      title=title, label=label, zorder=20, new=new, xmin=emin, xmax=emax,
+    #      **opts)
+    # _plot(dgroup.energy, bkg+offset, zorder=18, label='bkg', **opts)
+    # if show_e0:
+    #     _plot_axvline(dgroup.e0, zorder=2, size=3, label='E0',
+    #                   color=plotlabels.e0color, win=win, _larch=_larch)
+    #     disp = _getDisplay(win=win, _larch=_larch)
+    #     if disp is not None:
+    #         disp.panel.conf.draw_legend()
+    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 _plot_chik(spectrum):
+    # if kweight is None:
+    #     kweight = 0
+    #     xft = getattr(dgroup, 'xftf_details', None)
+    #     if xft is not None:
+    #         kweight = xft.call_args.get('kweight', 0)
+    #     #endif
+    # #endif
+    #
+    # chi = dgroup.chi * dgroup.k ** kweight
+    # opts = dict(win=win, show_legend=True, delay_draw=True, linewidth=3,
+    #             _larch=_larch)
+    # if label is None:
+    #     label = 'chi'
+    # #endif
+    # title = _get_title(dgroup, title=title)
+    # _plot(dgroup.k, chi+offset, xlabel=plotlabels.k,
+    #      ylabel=plotlabels.chikw.format(kweight), title=title,
+    #      label=label, zorder=20, new=new, xmax=kmax, **opts)
+    #
+    # if show_window and hasattr(dgroup, 'kwin'):
+    #     kwin = dgroup.kwin
+    #     if scale_window:
+    #         kwin = kwin*max(abs(chi))
+    #     _plot(dgroup.k, kwin+offset, zorder=12, label='window',  **opts)
+    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')
+
+
+class AutobkWindow(qt.QMainWindow):
+    def __init__(self, parent=None):
+        qt.QMainWindow.__init__(self, parent)
+
+        # xas object viewer
+        mapKeys = ['Mu', 'bkg', 'chie', 'k', 'chi', 'e0']
+        self.xasObjViewer = XasObjectViewer(mapKeys=mapKeys)
+        self.xasObjViewer._spectrumViews[0]._plot.getXAxis().setLabel("Energy (eV)")
+        self.xasObjViewer._spectrumViews[0]._plot.getYAxis().setLabel("Absorption (a.u.)")
+        self.setCentralWidget(self.xasObjViewer)
+        self._parametersWindow = _AutobkParameters(parent=self)
+        dockWidget = qt.QDockWidget(parent=self)
+
+        # parameters window
+        dockWidget.setWidget(self._parametersWindow)
+        self.addDockWidget(qt.Qt.RightDockWidgetArea, dockWidget)
+        dockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
+        dockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
+
+        # legend selector
+        self.legendDockWidget = LegendSelector.LegendsDockWidget(parent=self,
+                                                                 plot=self.xasObjViewer._spectrumViews[0]._plot)
+        self.legendDockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
+        self.legendDockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
+        self.addDockWidget(qt.Qt.RightDockWidgetArea, self.legendDockWidget)
+
+        # volume key selection
+        self.addDockWidget(qt.Qt.RightDockWidgetArea,
+                           self.xasObjViewer._mapView.keySelectionDocker)
+
+        # plot settings
+        for ope in (_plot_bkg, _plot_chik):
+            self.xasObjViewer._spectrumViews[0].addCurveOperation(ope)
+
+        self.setWindowFlags(qt.Qt.Widget)
+
+        # connect signal / slot
+        self.xasObjViewer.viewTypeChanged.connect(self._updateLegendView)
+
+        # set up
+        self._updateLegendView()
+
+    def getNCurves(self):
+        return len(self.xasObjViewer._spectrumViews._plot.getAllCurves())
+
+    def _updateLegendView(self):
+        index, viewType = self.xasObjViewer.getViewType()
+        self.legendDockWidget.setVisible(viewType is ViewType.spectrum)
+        self.xasObjViewer._mapView.keySelectionDocker.setVisible(viewType is ViewType.map)
+
+
+class AutobkOW(_ProcessForOrangeMixIn, OWWidget):
+    """
+    Widget used for signal extraction
+    """
+    name = "autobk"
+    id = "orange.widgets.xas.larch.autobk"
+    description = "background removal"
+    icon = "icons/autobk.png"
+    priority = 1
+    category = "esrfWidgets"
+    keywords = ["spectroscopy", "autobk", 'background']
+
+    want_main_area = True
+    resizing_enabled = True
+
+    inputs = [("spectra", XASObject, "process")]
+
+    outputs = [("spectra", XASObject), ("curves", tuple)]
+
+    process_function = xas.core.process.larch.autobk.Larch_autobk
+
+    _larchSettings = Setting(dict())
+    """Store the configuration of the PyMca XASClass"""
+
+    def __init__(self):
+        super().__init__()
+        self._latest_xas_obj = None
+        self._window = AutobkWindow(parent=self)
+        layout = gui.vBox(self.mainArea, 'fourier transform').layout()
+        layout.addWidget(self._window)
+        self._window.xasObjViewer.setWindowTitle('spectra')
+
+        # manage settings
+        if self._larchSettings != dict():
+            self._window._parametersWindow.setParameters(self._larchSettings)
+
+        # connect signals / slots
+        # TODO
+
+    def _updateProcess(self):
+        self._update_settings()
+        if self._latest_xas_obj:
+            self.process(self._latest_xas_obj)
+
+    def _update_settings(self):
+        self._pymcaSettings = self._window._parametersWindow.getParameters()
+
+    def process(self, xas_obj):
+        if xas_obj is None:
+            return
+
+        if not self._canProcess():
+            _logger.warning('There is some processing on going already, will'
+                            'not process the new dataset')
+
+        self._latest_xas_obj = xas_obj.copy()
+        self._startProcess()
+
+        # setup the normalization process
+        process_obj = QLarch_autobk()
+        process_obj._advancement.sigProgress.connect(self._setProgressValue)
+        process_obj.setProperties({
+            '_pymcaSettings': self._window._parametersWindow.getParameters()})
+
+        # update the processing thread
+        thread = self.getProcessingThread()
+        thread.init(process_obj=process_obj, xas_obj=xas_obj)
+        self._callback_finish = functools.partial(self._endProcess, xas_obj)
+        thread.finished.connect(self._callback_finish)
+        # start processing
+        thread.start(priority=qt.QThread.LowPriority)
+
+
+class QLarch_autobk(xas.core.process.larch.autobk.Larch_autobk):
+    """
+    Normalization able to give advancement using qt.Signal and QThreadPool
+    """
+
+    def __init__(self):
+        xas.core.process.larch.autobk.Larch_autobk.__init__(self)
+        self._advancement = QProgress('autobk')
+
+    def _pool_process(self, xas_obj):
+        self.pool = qt.QThreadPool()
+        self.pool.setMaxThreadCount(5)
+        for spectrum in xas_obj.spectra:
+            runnable = ProcessRunnable(fct=xas.core.process.larch.autobk.process_spectr_autobk,
+                                       spectrum=spectrum,
+                                       configuration=xas_obj.configuration,
+                                       callback=self._advancement.increaseAdvancement)
+            self.pool.start(runnable)
+        self.pool.waitForDone()

orangecontrib/xas/widgets/larch/icons/autobk.svg

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+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
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orangecontrib/xas/widgets/larch/icons/mback.svg

+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
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+   xmlns:dc="http://purl.org/dc/elements/1.1/"
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+  </g>
+</svg>

orangecontrib/xas/widgets/larch/mback.py

+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["H. Payno"]
+__license__ = "MIT"
+__date__ = "06/07/2019"
+
+
+import functools
+import logging
+from Orange.widgets import gui
+from Orange.widgets.settings import Setting
+from Orange.widgets.widget import OWWidget
+from silx.gui import qt
+from silx.gui.plot import LegendSelector
+import xas.core.process.larch.mback
+from orangecontrib.xas.process import _ProcessForOrangeMixIn
+from orangecontrib.xas.process import ProcessRunnable
+from xas.core.types import XASObject, Spectrum
+from xas.gui.XasObjectViewer import XasObjectViewer, _CurveOperation, ViewType
+from xas.gui.larch.mback import _MBackParameters
+from orangecontrib.xas.progress import QProgress
+
+_logger = logging.getLogger(__file__)
+
+
+
+def _plot_fpp(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    if not hasattr(spectrum, 'fpp'):
+        _logger.error('fpp has not been computed yet')
+        return
+    return _CurveOperation(x=spectrum.energy, y=spectrum.fpp, legend='fpp')
+
+
+def _plot_f2(spectrum):
+    assert isinstance(spectrum, Spectrum)
+    if not hasattr(spectrum, 'f2'):
+        _logger.error('f2 has not been computed yet')
+        return
+    return _CurveOperation(x=spectrum.energy, y=spectrum.f2, legend='f2')
+
+
+class MbackWindow(qt.QMainWindow):
+    def __init__(self, parent=None):
+        qt.QMainWindow.__init__(self, parent)
+
+        # xas object viewer
+        mapKeys = ['Mu', 'fpp', 'f2']
+        self.xasObjViewer = XasObjectViewer(mapKeys=mapKeys)
+        self.xasObjViewer._spectrumViews[0]._plot.getXAxis().setLabel("Energy (eV)")
+        self.setCentralWidget(self.xasObjViewer)
+        self._parametersWindow = _MBackParameters(parent=self)
+        dockWidget = qt.QDockWidget(parent=self)
+
+        # parameters window
+        dockWidget.setWidget(self._parametersWindow)
+        self.addDockWidget(qt.Qt.RightDockWidgetArea, dockWidget)
+        dockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
+        dockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
+
+        # legend selector
+        self.legendDockWidget = LegendSelector.LegendsDockWidget(parent=self,
+                                                                 plot=self.xasObjViewer._spectrumViews[0]._plot)
+        self.legendDockWidget.setAllowedAreas(qt.Qt.RightDockWidgetArea | qt.Qt.LeftDockWidgetArea)
+        self.legendDockWidget.setFeatures(qt.QDockWidget.NoDockWidgetFeatures)
+        self.addDockWidget(qt.Qt.RightDockWidgetArea, self.legendDockWidget)
+
+        # volume key selection
+        self.addDockWidget(qt.Qt.RightDockWidgetArea,
+                           self.xasObjViewer._mapView.keySelectionDocker)
+
+        # plot settings
+        for ope in (_plot_fpp, _plot_f2):
+            self.xasObjViewer._spectrumViews[0].addCurveOperation(ope)
+
+        self.setWindowFlags(qt.Qt.Widget)
+
+        # connect signal / slot
+        self.xasObjViewer.viewTypeChanged.connect(self._updateLegendView)
+
+        # set up
+        self._updateLegendView()
+
+    def _updateLegendView(self):
+        index, viewType = self.xasObjViewer.getViewType()
+        self.legendDockWidget.setVisible(viewType is ViewType.spectrum)
+        self.xasObjViewer._mapView.keySelectionDocker.setVisible(viewType is ViewType.map)
+
+
+class MbackOW(_ProcessForOrangeMixIn, OWWidget):
+    """
+    Widget used for signal extraction
+    """
+    name = "mback"
+    id = "orange.widgets.xas.larch.mback"
+    description = "Match mu(E) data for tabulated f''(E) using the MBACK " \
+                  "algorithm and, optionally, the Lee & Xiang extension"
+    icon = "icons/mback.png"
+    priority = 5
+    category = "esrfWidgets"
+    keywords = ["spectroscopy", "backm"]
+
+    want_main_area = True
+    resizing_enabled = True
+
+    inputs = [("spectra", XASObject, "process")]
+
+    outputs = [("spectra", XASObject), ("curves", tuple)]
+
+    process_function = xas.core.process.larch.mback.Larch_mback
+
+    _larchSettings = Setting(dict())
+    """Store the configuration of the larch configuration"""
+
+    def __init__(self):
+        super().__init__()
+        self._latest_xas_obj = None
+        self._window = MbackWindow(parent=self)
+        layout = gui.vBox(self.mainArea, 'backm').layout()
+        layout.addWidget(self._window)
+        self._window.xasObjViewer.setWindowTitle('spectra')
+
+        # manage settings
+        if self._larchSettings != dict():
+            self._window._parametersWindow.setParameters(self._larchSettings)
+
+        # connect signals / slots
+        self._window._parametersWindow.sigChanged.connect(self._updateProcess)
+
+    def _updateProcess(self):
+        self._update_settings()
+        if self._latest_xas_obj:
+            self.process(self._latest_xas_obj)
+
+    def _update_settings(self):
+        self._larchSettings = self._window._parametersWindow.getParameters()
+
+    def process(self, xas_obj):
+        if xas_obj is None:
+            return
+
+        if not self._canProcess():
+            _logger.warning('There is some processing on going already, will'
+                            'not process the new dataset')
+
+        self._latest_xas_obj = xas_obj.copy()
+        self._startProcess()
+
+        # setup the normalization process
+        process_obj = QLarch_mback()
+        process_obj._advancement