concatenated XAS spectra: skip N spectra and N start/end points

src/est/core/io.py

@@ -64,6 +64,8 @@ def read_from_url(
     I2_url: DataUrl | None = None,
     mu_ref_url: DataUrl | None = None,
     is_concatenated: bool = False,
+    skip_concatenated_n_points: int = 0,
+    skip_concatenated_n_spectra: int = 0,
     timeout: float = settings.DEFAULT_READ_TIMEOUT,
 ) -> XASObject:
     """
@@ -89,6 +91,8 @@ def read_from_url(
         I2_url=I2_url,
         mu_ref_url=mu_ref_url,
         is_concatenated=is_concatenated,
+        skip_concatenated_n_points=skip_concatenated_n_points,
+        skip_concatenated_n_spectra=skip_concatenated_n_spectra,
     )
     return read_from_input_information(input_information, timeout=timeout)
 

src/est/gui/xas_object_definition/dialog.py

@@ -196,6 +196,8 @@ class XASObjectDialog(qt.QWidget):
             I2_url=advanceHDF5Info.getI2Url(),
             mu_ref_url=advanceHDF5Info.getMuRefUrl(),
             is_concatenated=self._h5Dialog.isSpectraConcatenated(),
+            skip_concatenated_n_points=self._h5Dialog.getSkipConcatenatedNPoints(),
+            skip_concatenated_n_spectra=self._h5Dialog.getSkipConcatenatedNSpectra(),
         )
 
     def getChannelUrl(self):
@@ -210,3 +212,9 @@ class XASObjectDialog(qt.QWidget):
 
     def setConcatenatedSpectra(self, value: bool):
         self._h5Dialog.setConcatenatedSpectra(value)
+
+    def setSkipConcatenatedNPoints(self, value: int):
+        self._h5Dialog.setSkipConcatenatedNPoints(value)
+
+    def setSkipConcatenatedNSpectra(self, value: int):
+        self._h5Dialog.setSkipConcatenatedNSpectra(value)

src/est/gui/xas_object_definition/hdf5.py

@@ -72,6 +72,18 @@ class XASObjectFromH5(qt.QTabWidget):
     def setConcatenatedSpectra(self, value: bool):
         self._basicInformation._concatenatedCheckbox.setChecked(value)
 
+    def getSkipConcatenatedNPoints(self):
+        return self._basicInformation._skipConcatenatedNPoints.value()
+
+    def setSkipConcatenatedNPoints(self, value: int):
+        self._basicInformation._skipConcatenatedNPoints.setValue(value)
+
+    def getSkipConcatenatedNSpectra(self):
+        return self._basicInformation._skipConcatenatedNSpectra.value()
+
+    def setSkipConcatenatedNSpectra(self, value: int):
+        self._basicInformation._skipConcatenatedNSpectra.setValue(value)
+
 
 class _MandatoryXASObjectInfo(qt.QWidget):
     """Widget containing mandatory information"""
@@ -89,15 +101,42 @@ class _MandatoryXASObjectInfo(qt.QWidget):
 
         self._bufWidget = qt.QWidget(parent=self)
         self._bufWidget.setLayout(qt.QHBoxLayout())
+
+        # Spacer to push elements
         spacer = qt.QWidget(parent=self)
         spacer.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Minimum)
         self._bufWidget.layout().addWidget(spacer)
+
+        # Dimension selection widget
         self._dimensionSelection = _SpectraDimensions(parent=self._bufWidget)
         self._bufWidget.layout().addWidget(self._dimensionSelection)
+
+        # Concatenated checkbox
         self._concatenatedCheckbox = qt.QCheckBox(
             "Concatenated spectra", parent=self._bufWidget
         )
         self._bufWidget.layout().addWidget(self._concatenatedCheckbox)
+
+        # Labels and spin boxes
+        self._concatenatedWidget = qt.QWidget(parent=self)
+        self._concatenatedWidget.setLayout(qt.QVBoxLayout())
+
+        label1 = qt.QLabel("Skip first N concatenated spectra", parent=self._bufWidget)
+        self._skipConcatenatedNSpectra = qt.QSpinBox(parent=self._bufWidget)
+        self._concatenatedWidget.layout().addWidget(label1)
+        self._concatenatedWidget.layout().addWidget(self._skipConcatenatedNSpectra)
+
+        label2 = qt.QLabel(
+            "Skip N first and last points of concatenated spectra",
+            parent=self._bufWidget,
+        )
+        self._skipConcatenatedNPoints = qt.QSpinBox(parent=self._bufWidget)
+        self._concatenatedWidget.layout().addWidget(label2)
+        self._concatenatedWidget.layout().addWidget(self._skipConcatenatedNPoints)
+
+        self._bufWidget.layout().addWidget(self._concatenatedWidget)
+
+        # Add buffer widget to main layout
         self.layout().addWidget(self._bufWidget, 1, 1)
 
         # channel/energy url
@@ -122,19 +161,29 @@ class _MandatoryXASObjectInfo(qt.QWidget):
         self._configSelector._qLineEdit.editingFinished.connect(self._editingIsFinished)
         self._dimensionSelection.sigDimensionChanged.connect(self._editingIsFinished)
         self._energyUnit.currentIndexChanged.connect(self._editingIsFinished)
-        self._concatenatedCheckbox.clicked.connect(self._onBidimensionalCheckboxChange)
+        self._concatenatedCheckbox.stateChanged.connect(
+            self._onConcatenatedCheckboxChange
+        )
+        self._skipConcatenatedNPoints.valueChanged.connect(self._editingIsFinished)
+        self._skipConcatenatedNSpectra.valueChanged.connect(self._editingIsFinished)
 
         # expose API
         self.setDimensions = self._dimensionSelection.setDimensions
         self.getDimensions = self._dimensionSelection.getDimensions
 
-    def _onBidimensionalCheckboxChange(self):
-        self._dimensionSelection.setDisabled(self._concatenatedCheckbox.isChecked())
+        self._syncConcatenatedCheckbox()
+
+    def _syncConcatenatedCheckbox(self):
+        concatenated = self._concatenatedCheckbox.isChecked()
+        self._concatenatedWidget.setEnabled(concatenated)
+        self._dimensionSelection.setDisabled(concatenated)
+
+    def _onConcatenatedCheckboxChange(self):
+        self._syncConcatenatedCheckbox()
         self._editingIsFinished()
 
     def getSpectraUrl(self):
         """
-
         :return: the DataUrl of the spectra
         :rtype: DataUrl
         """
@@ -142,7 +191,6 @@ class _MandatoryXASObjectInfo(qt.QWidget):
 
     def getEnergyUrl(self):
         """
-
         :return: the DataUrl of energy / channel
         :rtype: DataUrl
         """

src/est/io/concatenated.py

 from __future__ import annotations
+
+from typing import Tuple, Dict, Any
+
+import pint
 import numpy
 
 from est import settings
@@ -10,14 +14,14 @@ from est.core.monotonic import piecewise_monotonic_interpolation_values
 
 def read_concatenated_xas(
     information: InputInformation, timeout: float = settings.DEFAULT_READ_TIMEOUT
-):
+) -> Tuple[numpy.ndarray, pint.Quantity, Dict[str, Any]]:
     """
     Method to read spectra acquired with the energy ramping up and down, with any number of repetitions.
 
-    When the scan is uni-directional, the ramp is always up. When the scan is concatenated the ramp is
+    When the scan is uni-directional, the ramp is always up. When the scan is bi-directional the ramp is
     alternating up and down.
 
-    The spectra are then interpolated to produce a 3D spectra (nb_energy_pts, nb_of_ramps, 1)
+    The spectra are then interpolated to produce a 3D data aray (nb_energy_pts, nb_of_ramps, 1).
 
     Limitations: the original spectra and energy datasets must be 1D.
     """
@@ -30,16 +34,25 @@ def read_concatenated_xas(
         config = None
 
     ramp_slices = split_piecewise_monotonic(raw_energy)
+
     energy = piecewise_monotonic_interpolation_values(raw_energy, ramp_slices)
 
+    if information.skip_concatenated_n_spectra:
+        ramp_slices = ramp_slices[information.skip_concatenated_n_spectra :]
+
     interpolated_spectra = numpy.zeros(
         (len(energy), len(ramp_slices), 1), dtype=raw_spectra.dtype
     )
     for i, ramp_slice in enumerate(ramp_slices):
+        raw_energy_i = raw_energy[ramp_slice]
+        raw_spectrum_i = raw_spectra[ramp_slice]
+        if information.skip_concatenated_n_points:
+            raw_spectrum_i[: information.skip_concatenated_n_points] = numpy.nan
+            raw_spectrum_i[-information.skip_concatenated_n_points :] = numpy.nan
         interpolated_spectra[:, i, 0] = numpy.interp(
             energy,
-            raw_energy[ramp_slice],
-            raw_spectra[ramp_slice],
+            raw_energy_i,
+            raw_spectrum_i,
             left=numpy.nan,
             right=numpy.nan,
         )

src/est/io/information.py

@@ -23,6 +23,8 @@ class InputInformation:
         I2_url: DataUrl | None = None,
         mu_ref_url: DataUrl | None = None,
         is_concatenated: bool = False,
+        skip_concatenated_n_points: int = 0,
+        skip_concatenated_n_spectra: int = 0,
     ):
         # main information
         self.spectra_url = spectra_url
@@ -31,6 +33,8 @@ class InputInformation:
         self.dimensions = dimensions_mod.parse_dimensions(dimensions)
         self.energy_unit = energy_unit
         self.is_concatenated = is_concatenated
+        self.skip_concatenated_n_points = skip_concatenated_n_points
+        self.skip_concatenated_n_spectra = skip_concatenated_n_spectra
 
         # "fancy information"
         self.I0_url = I0_url
@@ -56,6 +60,8 @@ class InputInformation:
             "I2_url": dump_url(self.I2_url),
             "mu_ref_url": dump_url(self.mu_ref_url),
             "is_concatenated": self.is_concatenated,
+            "skip_concatenated_n_points": self.skip_concatenated_n_points,
+            "skip_concatenated_n_spectra": self.skip_concatenated_n_spectra,
         }
 
     @staticmethod
@@ -79,4 +85,6 @@ class InputInformation:
             I2_url=load_url("I2_url"),
             mu_ref_url=load_url("mu_ref_url"),
             is_concatenated=ddict.get("is_concatenated", False),
+            skip_concatenated_n_points=ddict.get("skip_concatenated_n_points", 0),
+            skip_concatenated_n_spectra=ddict.get("skip_concatenated_n_spectra", 0),
         )

src/orangecontrib/est/widgets/utils/xas_input.py

@@ -80,10 +80,15 @@ class XASInputOW(OWEwoksWidgetNoThread, ewokstaskclass=ReadXasObject):
                 self._inputDialog.setEnergyUrl(input_information.channel_url)
             if input_information.mu_ref_url is not None:
                 advanceHDF5Info.setMuRefUrl(input_information.mu_ref_url)
-            if input_information.is_concatenated is not None:
-                self._inputDialog.getMainWindow().setConcatenatedSpectra(
-                    input_information.is_concatenated
-                )
+            self._inputDialog.getMainWindow().setSkipConcatenatedNPoints(
+                input_information.skip_concatenated_n_points
+            )
+            self._inputDialog.getMainWindow().setSkipConcatenatedNSpectra(
+                input_information.skip_concatenated_n_spectra
+            )
+            self._inputDialog.getMainWindow().setConcatenatedSpectra(
+                input_information.is_concatenated
+            )
         else:
             input_type = est.io.InputType.ascii_spectrum
             self._inputDialog.setAsciiFile(input_information.spectra_url.file_path())