diff --git a/src/est/core/io.py b/src/est/core/io.py
index 7d6c5f11e233ef12d712abde5d022a84798e199e..fed17229b2d862023d96ae801e253ec44810d76b 100644
--- a/src/est/core/io.py
+++ b/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)
diff --git a/src/est/core/process/plotspectrumdata.py b/src/est/core/process/plotspectrumdata.py
index fd6a67aadc623a8edfafb759013893c036451f85..50f0a61ddbaf210bcff796a60960d35b8e88647e 100644
--- a/src/est/core/process/plotspectrumdata.py
+++ b/src/est/core/process/plotspectrumdata.py
@@ -106,7 +106,7 @@ class PlotSpectrumData(
output_names=["plot_data"],
):
def run(self):
- spectrum = next(iter(self.inputs.xas_obj.spectra.data.flat))
- self.outputs.plot_data = process_plotspectrumdata(
- spectrum, plot_names=self.inputs.plot_names
- )
+ self.outputs.plot_data = [
+ process_plotspectrumdata(spectrum, plot_names=self.inputs.plot_names)
+ for spectrum in self.inputs.xas_obj.spectra.data.flat
+ ]
diff --git a/src/est/core/types/spectra.py b/src/est/core/types/spectra.py
index b23047417abee2b414cb48dda0a18d84960be5c3..17362e7ab4b79584b79ba6acc0a22479965e7ac2 100644
--- a/src/est/core/types/spectra.py
+++ b/src/est/core/types/spectra.py
@@ -141,55 +141,54 @@ class Spectra:
if len(self.data.flat) == 0:
return None
- else:
- def allocate_array(relative_to_len):
- if relative_to_len is not None:
- return numpy.zeros((relative_to_len, len(self.data.flat)))
- else:
- return numpy.zeros(len(self.data.flat))
-
- key = str(data_info)
- array = None
- for i_spectrum, spectrum in enumerate(self.data.flat):
- try:
- if "." in key:
- subkeys = key.split(".")
- key_ = subkeys[-1]
- subkeys = subkeys[:-1]
- value = get_param(spectrum, subkeys[0])
- for subkey in subkeys[1:]:
- value = get_param(value, subkey)
- value = get_param(value, key_)
- else:
- value = get_param(spectrum, key)
- except Exception:
- _logger.info("fail to access to {}".format(key))
- break
+ def allocate_array(relative_to_len):
+ if relative_to_len is not None:
+ return numpy.zeros((relative_to_len, len(self.data.flat)))
+ else:
+ return numpy.zeros(len(self.data.flat))
+
+ key = str(data_info)
+ array = None
+ for i_spectrum, spectrum in enumerate(self.data.flat):
+ try:
+ if "." in key:
+ subkeys = key.split(".")
+ key_ = subkeys[-1]
+ subkeys = subkeys[:-1]
+ value = get_param(spectrum, subkeys[0])
+ for subkey in subkeys[1:]:
+ value = get_param(value, subkey)
+ value = get_param(value, key_)
else:
- if isinstance(value, pint.Quantity):
- value = value.m_as(ur.eV)
- if symboltable is not None and isinstance(value, symboltable.Group):
- _logger.info("pass larch details, not managed for now")
- continue
- # create array if necessary
- if array is None:
- if relative_to is None:
- array = allocate_array(relative_to_len=None)
- elif value is None:
- array = allocate_array(relative_to_len=None)
- else:
- array = allocate_array(relative_to_len=len(value))
- if relative_to is not None:
- array[:, i_spectrum] = value
- else:
- array[i_spectrum] = value
- shape = list(self.data.shape)
- shape.insert(0, -1)
+ value = get_param(spectrum, key)
+ except Exception:
+ _logger.info("fail to access to {}".format(key))
+ break
+
+ if isinstance(value, pint.Quantity):
+ value = value.m_as(ur.eV)
+ if symboltable is not None and isinstance(value, symboltable.Group):
+ _logger.info("pass larch details, not managed for now")
+ continue
+
if array is None:
- return array
+ if relative_to is None or value is None:
+ array = allocate_array(relative_to_len=None)
+ else:
+ array = allocate_array(relative_to_len=len(value))
+
+ if relative_to is not None:
+ array[:, i_spectrum] = value
else:
- return array.reshape(shape)
+ array[i_spectrum] = value
+
+ if array is None:
+ return array
+
+ shape = list(self.data.shape)
+ shape.insert(0, -1)
+ return array.reshape(shape)
def keys(self) -> tuple:
"""
diff --git a/src/est/core/types/xasobject.py b/src/est/core/types/xasobject.py
index 118bc1e0015810367019a6dd8d5ff66cf8fab25e..4de131bd4e60e9c1b31adcdd32d994059a4ecd70 100644
--- a/src/est/core/types/xasobject.py
+++ b/src/est/core/types/xasobject.py
@@ -180,7 +180,7 @@ class XASObject:
return res
def absorbed_beam(self) -> numpy.ndarray:
- return self.spectra.map_to(data_info="mu")
+ return self.spectra.map_to("mu")
def load_from_dict(self, ddict: dict) -> XASObject:
"""load XAS values from a dict"""
diff --git a/src/est/core/utils/converter.py b/src/est/core/utils/converter.py
index 2e811d07c45339980c5aa5b086f1ea6c360aabb6..0d3deced3084ded0f14068fda65ff5f593143f6b 100644
--- a/src/est/core/utils/converter.py
+++ b/src/est/core/utils/converter.py
@@ -32,7 +32,7 @@ class Converter:
)
# TODO: prendre normalized_mu and normalized_energy if exists,
# otherwise take mu and energy...
- spectra = xas_object.spectra.map_to(data_info="mu")
+ spectra = xas_object.spectra.map_to("mu")
# invert dimensions and axis to fit spectroscopy add-on
X = spectra.reshape((spectra.shape[0], -1))
X = numpy.swapaxes(X, 0, 1)
diff --git a/src/est/gui/XasObjectViewer.py b/src/est/gui/XasObjectViewer.py
index 649985d29341dca07696c9de44185f321994a204..c6667826e5f3144ca2d8bf0a6b3155773c94a4be 100644
--- a/src/est/gui/XasObjectViewer.py
+++ b/src/est/gui/XasObjectViewer.py
@@ -212,9 +212,7 @@ class MapViewer(qt.QWidget):
if self._xasObj is None:
return
# set the map view
- spectra_volume = self._xasObj.spectra.map_to(
- data_info=self.getActiveKey(),
- )
+ spectra_volume = self._xasObj.spectra.map_to(self.getActiveKey())
self._mainWindow.setStack(spectra_volume)
def getPlot(self):
diff --git a/src/est/gui/xas_object_definition/dialog.py b/src/est/gui/xas_object_definition/dialog.py
index 3a2d3f56e4e128f6ad8538a9f45312feffb99a60..3bbd35fbb30090ec127873b70d0d908c71233608 100644
--- a/src/est/gui/xas_object_definition/dialog.py
+++ b/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)
diff --git a/src/est/gui/xas_object_definition/hdf5.py b/src/est/gui/xas_object_definition/hdf5.py
index b93f8536545e10c5f9ff6332505c5c8c04368a11..6984c8c88571ca18bcc73c6f6fa4cd804f4f1c14 100644
--- a/src/est/gui/xas_object_definition/hdf5.py
+++ b/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
"""
diff --git a/src/est/io/concatenated.py b/src/est/io/concatenated.py
index 0e7f8a36bae54978efe81ed6920fd44aa524d4bf..156f9bac5a8030763dbe60dddc818fd127a94305 100644
--- a/src/est/io/concatenated.py
+++ b/src/est/io/concatenated.py
@@ -1,5 +1,10 @@
from __future__ import annotations
+
+from typing import Tuple, Dict, Any
+
+import pint
import numpy
+import numpy.ma
from est import settings
from est.io.information import InputInformation
@@ -10,14 +15,14 @@ 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.
"""
@@ -30,18 +35,30 @@ def read_concatenated_xas(
config = None
ramp_slices = split_piecewise_monotonic(raw_energy)
+
energy = piecewise_monotonic_interpolation_values(raw_energy, ramp_slices)
- interpolated_spectra = numpy.zeros(
+ if information.skip_concatenated_n_spectra:
+ ramp_slices = ramp_slices[information.skip_concatenated_n_spectra :]
+
+ interpolated_spectra = numpy.ma.masked_all(
(len(energy), len(ramp_slices), 1), dtype=raw_spectra.dtype
)
for i, ramp_slice in enumerate(ramp_slices):
- interpolated_spectra[:, i, 0] = numpy.interp(
+ 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
+ spectrum_i = numpy.interp(
energy,
- raw_energy[ramp_slice],
- raw_spectra[ramp_slice],
+ raw_energy_i,
+ raw_spectrum_i,
left=numpy.nan,
right=numpy.nan,
)
+ interpolated_spectra[:, i, 0] = numpy.ma.masked_array(
+ spectrum_i, mask=~numpy.isfinite(spectrum_i)
+ )
return interpolated_spectra, energy * information.energy_unit, config
diff --git a/src/est/io/information.py b/src/est/io/information.py
index c33d0df6b3445a84e25daee157d4be2e2faeb724..b84493896418f880b8de06720b28e02636228990 100644
--- a/src/est/io/information.py
+++ b/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),
)
diff --git a/src/est/tests/test_plotspectrumdata.py b/src/est/tests/test_plotspectrumdata.py
index e17d5d3d8ea5c16eda779d4483e758aa7cb8e337..2805b96d51332e7da40a80e316ba345e8d2196c8 100644
--- a/src/est/tests/test_plotspectrumdata.py
+++ b/src/est/tests/test_plotspectrumdata.py
@@ -66,8 +66,12 @@ def test_larch_plotspectrumdata(filename_cu_from_pymca):
)
result = execute_graph(_LARCH_WORKFLOW, inputs=inputs)
- assert len(result["plot_data"]) == 7
- for name, data in result["plot_data"].items():
+ assert len(result["plot_data"]) == 1
+
+ scan_data = result["plot_data"][0]
+
+ assert len(scan_data) == 7
+ for name, data in scan_data.items():
if name in ("chi", "chi_weighted_k"):
n = 324
elif name == "ft_mag":
@@ -79,13 +83,13 @@ def test_larch_plotspectrumdata(filename_cu_from_pymca):
assert data["xlabel"]
assert data["ylabel"]
- assert "k^2" in result["plot_data"]["chi_weighted_k"]["ylabel"]
+ assert "k^2" in scan_data["chi_weighted_k"]["ylabel"]
if False:
import matplotlib.pyplot as plt
fig, axs = plt.subplots(2, 3, figsize=(10, 10), constrained_layout=True)
- for data, ax in zip(result["plot_data"].values(), axs.flatten()):
+ for data, ax in zip(scan_data.values(), axs.flatten()):
ax.plot(data["x"], data["y"])
ax.set_xlabel(data["xlabel"])
ax.set_ylabel(data["ylabel"])
diff --git a/src/est/tests/test_roi.py b/src/est/tests/test_roi.py
index 47b710e9dc5066e2ad744934a337abf7cdcebdf9..750dc2f2ea6e552ebde72315eb8203ddc568811e 100644
--- a/src/est/tests/test_roi.py
+++ b/src/est/tests/test_roi.py
@@ -22,7 +22,7 @@ def test_roi(tmpdir):
dimensions=(2, 1, 0),
)
- original_spectra = xas_obj.spectra.map_to(data_info="mu").copy()
+ original_spectra = xas_obj.spectra.map_to("mu").copy()
assert original_spectra.shape == (16, 100, 30)
res_xas_obj = xas_roi(
xas_obj,
@@ -30,6 +30,6 @@ def test_roi(tmpdir):
roi_size=(10, 20),
)
assert res_xas_obj.n_spectrum == 20 * 10
- reduces_spectra = res_xas_obj.spectra.map_to(data_info="mu").copy()
+ reduces_spectra = res_xas_obj.spectra.map_to("mu").copy()
assert reduces_spectra.shape == (16, 20, 10)
numpy.testing.assert_array_equal(original_spectra[:, 50:70, 20:30], reduces_spectra)
diff --git a/src/est/tests/test_types.py b/src/est/tests/test_types.py
index 5bc0f4f40687440360acc6e1e1773b4d9ffd8800..9fdc0ef8fa36da3add90fac4caa883d33fbdd9fb 100644
--- a/src/est/tests/test_types.py
+++ b/src/est/tests/test_types.py
@@ -75,7 +75,7 @@ def test_create_from_several_spectrums(tmpdir):
)
obj2 = XASObject.from_dict(ddict)
assert xas_obj.n_spectrum == obj2.n_spectrum
- obj2_mu_spectra = obj2.spectra.map_to(data_info="mu")
+ obj2_mu_spectra = obj2.spectra.map_to("mu")
numpy.testing.assert_array_equal(original_spectra, obj2_mu_spectra)
assert obj2 == xas_obj
diff --git a/src/est/tests/test_xas_object.py b/src/est/tests/test_xas_object.py
index ddba00414b501d0f5ebff0b4e7c6430de077b757..79f1116c7e4fee8a621b45cfa1ea435309e694c9 100644
--- a/src/est/tests/test_xas_object.py
+++ b/src/est/tests/test_xas_object.py
@@ -66,7 +66,7 @@ def test_create_from_several_spectrums(serialize_data):
)
obj2 = XASObject.from_dict(ddict)
assert xas_obj.n_spectrum == obj2.n_spectrum
- obj2_mu_spectra = obj2.spectra.map_to(data_info="mu")
+ obj2_mu_spectra = obj2.spectra.map_to("mu")
numpy.testing.assert_array_equal(original_spectra, obj2_mu_spectra)
assert obj2 == xas_obj
diff --git a/src/orangecontrib/est/widgets/utils/xas_input.py b/src/orangecontrib/est/widgets/utils/xas_input.py
index 53cefd60146af629fa5a10c4a0729a4b36a7ac32..37dc07ad22f38ba2cbcba0c8e8b53e4c67b1b79b 100644
--- a/src/orangecontrib/est/widgets/utils/xas_input.py
+++ b/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())