.flake8

+[flake8]
+extend-ignore = E203,E402,E501,E701,W503
+max-line-length = 88
+exclude = [".eggs"]

.flake8_nb

+[flake8_nb]
+ignore = E501, E203, W503, E402
+max-line-length = 88

.gitignore

@@ -7,6 +7,7 @@
 !.gitignore
 !.gitlab-ci.yml
 !.readthedocs.yaml
+!.flake8
 
 # Byte / compiled / optimized
 *.py[cod]

.gitlab-ci.yml

 include:
-  - project: workflow/ewoksadmin/ewoksci
+  - project: dau/ci/pyci
     file: .gitlab-ci-template.yml
 
 variables:
-  WARNING1: "ignore::DeprecationWarning:silx.resources"  # Fix in https://github.com/silx-kit/silx/pull/4078
-  WARNING2: "ignore::DeprecationWarning:pkg_resources"  # Distribution.activate
-  WARNING3: "ignore::DeprecationWarning:Orange.util"  # Fix in https://github.com/biolab/orange3/commit/671f184be00169e0a5196e9871ee0156dd35c19f
-  WARNING4: "ignore::DeprecationWarning:orangewidget.gui"  # Fix in https://github.com/biolab/orange-widget-base/commit/2c6b4cfbba035f7f89bb886a02d8330f2710ce7d
-  WARNING5: "ignore::DeprecationWarning:jupyter_client.session"
-  WARNING6: "ignore::DeprecationWarning:silx.gui.widgets.ElidedLabel"
-  IGNORE_WARNINGS: "-W ${WARNING1} -W ${WARNING2} -W ${WARNING3} -W ${WARNING4} -W ${WARNING5} -W ${WARNING6}"
+  WARNING1: 'ignore::DeprecationWarning:silx.resources' # Fix in https://github.com/silx-kit/silx/pull/4078
+  WARNING2: 'ignore::DeprecationWarning:pkg_resources' # Distribution.activate
+  WARNING3: 'ignore::DeprecationWarning:Orange.util' # Fix in https://github.com/biolab/orange3/commit/671f184be00169e0a5196e9871ee0156dd35c19f
+  WARNING4: 'ignore::DeprecationWarning:orangewidget.gui' # Fix in https://github.com/biolab/orange-widget-base/commit/2c6b4cfbba035f7f89bb886a02d8330f2710ce7d
+  WARNING5: 'ignore::DeprecationWarning:jupyter_client.session'
+  WARNING6: 'ignore::DeprecationWarning:silx.gui.widgets.ElidedLabel'
+  WARNING7: 'ignore::DeprecationWarning:orangecanvas.scheme.readwrite' # https://github.com/biolab/orange-canvas-core/issues/304
+  WARNING8: "ignore::DeprecationWarning:orangecanvas.utils.localization"
+  WARNING9: "ignore::DeprecationWarning:orangecanvas.utils.localization.si"
+  IGNORE_WARNINGS: '-W ${WARNING1} -W ${WARNING2} -W ${WARNING3} -W ${WARNING4} -W ${WARNING5} -W ${WARNING6} -W ${WARNING7} -W ${WARNING8} -W ${WARNING9}'
 
 flake8_nb:
   extends: .flake8_nb
@@ -18,48 +21,69 @@ test-3.8:
   extends: .test-3.8_glx
   timeout: 20m
   variables:
-    PYTEST_WARNINGS: "-W error ${IGNORE_WARNINGS}"
-    PIP_INSTALL_OPTIONS: "--pre -e"  # because of --import-mode=importlib"
+    PYTEST_WARNINGS: '-W error ${IGNORE_WARNINGS}'
+    PIP_INSTALL_OPTIONS: '-e'  # no --pre because of Orange3 and cython 3.1.0a1, -e because of --import-mode=importlib"
 
-test-3.8-minimal:
-  extends: .test-3.8_glx
+test-3.9:
+  extends: .test-3.9_glx
   timeout: 20m
   variables:
-    PYTEST_WARNINGS: "-W error ${IGNORE_WARNINGS}"
-    PYTEST_COV: ""
+    PYTEST_WARNINGS: '-W error ${IGNORE_WARNINGS}'
+    PIP_INSTALL_OPTIONS: '--pre -e' # -e because of --import-mode=importlib"
 
-test-3.8-pymca:
-  extends: .test-3.8_glx
+test-3.9-minimal:
+  extends: .test-3.9_glx
   timeout: 20m
   variables:
-    PYTEST_WARNINGS: "-W error ${IGNORE_WARNINGS}"
-    PYTEST_COV: ""
+    PYTEST_WARNINGS: '-W error ${IGNORE_WARNINGS}'
+    PYTEST_COV: ''
 
-test-3.8-larch:
-  extends: .test-3.8_glx
+test-3.9-pymca:
+  extends: .test-3.9_glx
   timeout: 20m
   variables:
-    PYTEST_WARNINGS: "-W error ${IGNORE_WARNINGS}"
-    PYTEST_COV: ""
+    PYTEST_WARNINGS: '-W error ${IGNORE_WARNINGS}'
+    PYTEST_COV: ''
 
-test-3.8-larch-example:
-  extends: .test-3.8_glx
+test-3.9-larch:
+  extends: .test-3.9_glx
+  timeout: 20m
+  variables:
+    PYTEST_WARNINGS: '-W error ${IGNORE_WARNINGS}'
+    PYTEST_COV: ''
+
+test-3.9-larch-example:
+  extends: .test-3.9_glx
   script:
     - python -m pip install --pre .[larch] pyqt5
     - ./scripts/larch_example/run.sh
 
+test-3.11:
+  extends: .test-3.10_glx
+  timeout: 20m
+  variables:
+    PYTEST_WARNINGS: '-W error ${IGNORE_WARNINGS}'
+    PIP_INSTALL_OPTIONS: '--pre -e' # -e because of --import-mode=importlib"
+
+test-3.12:
+  extends: .test-3.12_glx
+  timeout: 20m
+  variables:
+    PYTEST_WARNINGS: '-W error ${IGNORE_WARNINGS}'
+    PIP_INSTALL_OPTIONS: '--pre -e' # -e because of --import-mode=importlib"
+
 build_sdist:
   extends: .build_sdist
 
 test_sdist-3.9:
   extends: .test_sdist-3.9_glx
   variables:
-    PYTEST_WARNINGS: "-W error ${IGNORE_WARNINGS}"
+    PYTEST_WARNINGS: '-W error ${IGNORE_WARNINGS}'
 
 build_doc:
   extends: .build_doc
   script:
-    - python -m pip install sphinx  # solves issue with pip dependency solver
+    - python -m pip install sphinx # solves issue with pip dependency solver
     - python -m pip install .[doc]
     - sphinx-build doc html
 
@@ -68,3 +92,9 @@ pages:
 
 assets:
   extends: .assets
+
+pypi:
+  extends: .pypi
+
+testpypi:
+  extends: .testpypi

CHANGELOG.md

+# CHANGELOG.md
+
+## Unreleased
+
+## 1.0.0
+
+Changes:
+
+- Add rebinning to the `Larch_autobk` task.
+- Support concatenated multi-XAS scans that can be uni- or bi-directional.
+- Support concatenated multi-XAS scans with fixed section size as well as monotonic section detection.
+
+New Features:
+
+- Ewoks task `SplitBlissScan` to split concatenated multi-XAS scan HDF5 data.
+- `get_data_from_url` supports online data access.
+
+## 0.7.2
+
+Bug fixes:
+
+- Fix icon reading
+
+## 0.7.1
+
+New Features:
+
+- Add support for Python 3.12
+
+## 0.7.0
+
+New Features:
+
+- Read bi-directional scan data with monotonic section detection.
+
+Changes:
+
+- Remove `pkg_resources` usage and related changes in Orange packages
+- Refactor HDF5 and ASCII data reading

README.md

 # Est: Spectroscopy workflows
 
-`est` is a library providing tools to define a workflow of treatments for X-ray Absorption Structure analysis.
-Treatments are based on eather [PyMca](https://github.com/vasole/pymca)_ or [Larch](https://xraypy.github.io/xraylarch/)
+`est` is a library to define workflows for X-ray Absorption Structure analysis.
+The analysis can be based on either [PyMca](https://github.com/vasole/pymca) or [Larch](https://xraypy.github.io/xraylarch/)
 
-The library offers a convenient object for connecting those two.
+![An example workflow](https://ewoksest.readthedocs.io/en/latest/_images/workflow_example.png)
 
-An [Orange3](https://github.com/biolab/orange3) add-on is also provided by the library to help user defining graphically the workflow they want to process.
+## Quick start
 
-## Installation
-
-``` python
-pip install est[full]
+```python
+pip install est[full] pyqt5
+ewoks-canvas
 ```
 
-## Test
-
-```bash
-pytest --pyargs est.tests
-```
+See then the _Example workflows_ to get started.
 
 ## Documentation
 

doc/conf.py

 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-from est import __version__ as release
+from importlib.metadata import version as get_version
 
 project = "est"
+release = get_version(project)
 version = ".".join(release.split(".")[:2])
-copyright = "2019-2023, ESRF"
+copyright = "2019-2024, ESRF"
 author = "ESRF"
 docstitle = f"{project} {version}"
 

doc/index.rst

+Summary
+-------
+
 `est` provides `ewoks tasks <https://ewoks.readthedocs.io/en/latest>`_ that can be connected
 together to define a workflow for X-ray Absorption Structure analysis. Tasks are based on
 either `PyMca <https://github.com/vasole/pymca>`_ or `Larch <https://xraypy.github.io/xraylarch/>`_.
@@ -14,3 +17,4 @@ help user defining graphically the workflow they want to run.
    user_guide/index.rst
    api.rst
    app/index.rst
+   CHANGELOG.rst

pyproject.toml

 [build-system]
-requires = [
-    "setuptools>=46.4<63",
-    "wheel",
-]
+requires = ["setuptools>=46.4"]
 build-backend = "setuptools.build_meta"
 
 [tool.pytest.ini_options]
 # consider_namespace_packages = true  # for pytest>=8.1
-addopts = "--import-mode=importlib"  # for all pytest versions, pytest-cov needs `pip install -e .`
+addopts = "--import-mode=importlib" # for all pytest versions, pytest-cov needs `pip install -e .`
+
+[project]
+name = "est"
+version = "1.0.0"
+keywords = ['orange3 add-on', 'ewoks']
+authors = [{name = "ESRF", email = "dau-pydev@esrf.fr"}]
+description = "Spectroscopy workflows"
+readme = {file = "README.md", content-type = "text/markdown"}
+license = {file = "LICENSE"}
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+]
+requires-python = ">=3.8"
+dependencies = [
+    "numpy",
+    "scipy",
+    "h5py >=3.1",
+    "silx >=0.15",
+    "Pint",
+    "ewoks[orange] >=0.1",
+    "ewoksorange >=0.7.0",
+    "importlib_resources; python_version < '3.9'",
+]
+
+[project.urls]
+Homepage = "https://gitlab.esrf.fr/workflow/ewoksapps/est/"
+Documentation = "https://ewoksest.readthedocs.io/"
+Repository = "https://gitlab.esrf.fr/workflow/ewoksapps/est/"
+Issues = "https://gitlab.esrf.fr/workflow/ewoksapps/est/issues"
+Changelog = "https://gitlab.esrf.fr/workflow/ewoksapps/est/-/blob/main/CHANGELOG.md"
+
+[project.optional-dependencies]
+pymca = [
+    "pymca >=5.8.1",
+]
+larch = [
+    "xraylarch >=0.9.71",
+]
+orange = [
+    "ewoksorange[orange] >=0.7.0",
+]
+full = [
+    "est[pymca]",
+    "est[larch]",
+    "est[orange]",
+]
+test_no_larch_or_pymca = [
+    "pytest >=7",
+    "testbook",
+    "ipykernel",
+    "pyqt5",
+]
+test = [
+    "est[full]",
+    "est[test_no_larch_or_pymca]",
+]
+dev = [
+    "est[test]",
+    "black >=25",
+    "flake8 >=4",
+    "flake8_nb >= 0.3.1",
+    "pillow >= 10.0",
+]
+doc = [
+    "est[test]",
+    "est[full]",
+    "sphinx >=4.5",
+    "sphinx-autodoc-typehints >=1.16",
+    "ipykernel",
+    "nbsphinx",
+    "nbsphinx_link",
+    "docutils < 0.21",  # v0.21 incompatible with nbsphinx_link: https://github.com/vidartf/nbsphinx-link/issues/22
+    "pydata_sphinx_theme",
+]
+
+[tool.setuptools]
+package-dir = { "" = "src" }
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"*"= ['*.ows', '*.png', '*.svg', '*.dat', '*.xmu', '*.ipynb']
+
+[tool.coverage.run]
+omit = ['*/tests/*']
+
+[project.scripts]
+est = "est.__main__:main"
+
+[project.entry-points."orange3.addon"]
+"est-add-on" = "orangecontrib.est"
+
+[project.entry-points."orange.widgets"]
+"Est" = "orangecontrib.est.widgets"
+
+[project.entry-points."orange.widgets.tutorials"]
+"Est" = "orangecontrib.est.tutorials"
+
+[project.entry-points."orange.canvas.help"]
+"html-index" = "orangecontrib.est.widgets:WIDGET_HELP_PATH"
+
+[project.entry-points."ewoks.tasks.class"]
+"est.core.process.*" = "est1"
+"est.core.process.*.*" = "est2"

scripts/generate_resources.py

@@ -3,9 +3,6 @@ from pathlib import Path
 from est import resources
 
 
-RESOURCE_ROOT = Path(__file__).resolve().parent.parent / "est" / "resources"
-
-
 def download(url: str, filename: Path):
     with urlopen(url) as response:
         with open(filename, "wb") as out_file:
@@ -16,23 +13,23 @@ def download(url: str, filename: Path):
 
 def download_larch_cu():
     url = "https://raw.githubusercontent.com/xraypy/xraylarch/master/examples/xafs/cu_rt01.xmu"
-    filename = RESOURCE_ROOT / "exafs" / "cu_rt01.xmu"
-    download(url, filename)
-    resources.generate_resource("exafs/cu_rt01.xmu", overwrite=True)
+    with resources.resource_path("exafs", "cu_rt01.xmu") as filename:
+        download(url, filename)
+    resources.generate_resource("exafs", "cu_rt01.xmu", overwrite=True)
 
 
 def download_pymca_cu():
     url = "https://raw.githubusercontent.com/vasole/pymca/master/PyMca5/PyMcaData/EXAFS_Cu.dat"
-    filename = RESOURCE_ROOT / "exafs" / "EXAFS_Cu.dat"
-    download(url, filename)
-    resources.generate_resource("exafs/EXAFS_Cu.dat", overwrite=True)
+    with resources.resource_path("exafs", "EXAFS_Cu.dat") as filename:
+        download(url, filename)
+    resources.generate_resource("exafs", "EXAFS_Cu.dat", overwrite=True)
 
 
 def download_pymca_ge():
     url = "https://raw.githubusercontent.com/vasole/pymca/master/PyMca5/PyMcaData/EXAFS_Ge.dat"
-    filename = RESOURCE_ROOT / "exafs" / "EXAFS_Ge.dat"
-    download(url, filename)
-    resources.generate_resource("exafs/EXAFS_Ge.dat", overwrite=True)
+    with resources.resource_path("exafs", "EXAFS_Ge.dat") as filename:
+        download(url, filename)
+    resources.generate_resource("exafs", "EXAFS_Ge.dat", overwrite=True)
 
 
 if __name__ == "__main__":

scripts/split_bliss_scan.py

+from ewokscore import execute_graph
+from ewoksutils.task_utils import task_inputs
+
+if __name__ == "__main__":
+
+    inputs = {
+        "filename": "/data/scisoft/ewoks/ch7280/id24-dcm/20250131/RAW_DATA/Ru_WVC1/Ru_WVC1_1_RT_air/Ru_WVC1_1_RT_air.h5",
+        "scan_number": 1,
+        "monotonic_channel": "measurement/energy_enc",
+        "out_filename": "/tmp/test.h5",
+        "subscan_size": 3001,
+    }
+
+    node = {
+        "task_type": "class",
+        "task_identifier": "est.core.process.split.SplitBlissScan",
+    }
+    graph = {"graph": {"graph_version": "1.1", "id": "split"}, "nodes": [node]}
+    print(execute_graph(graph, inputs=task_inputs(inputs=inputs)))

setup.cfg

-[metadata]
-name = est
-version = attr: est.__version__
-author = data analysis unit
-author_email = henri.payno@esrf.fr
-description = Spectroscopy workflows
-long_description = file: README.md
-long_description_content_type = text/markdown
-license = MIT
-url = https://gitlab.esrf.fr/workflow/ewoksapps/est
-project_urls = 
-    Source = https://gitlab.esrf.fr/workflow/ewoksapps/est/
-    Documentation = https://ewoksest.readthedocs.io/
-    Tracker = https://gitlab.esrf.fr/workflow/ewoksapps/est/issues/
-classifiers = 
-    Intended Audience :: Science/Research
-    License :: OSI Approved :: MIT License
-    Programming Language :: Python :: 3
-keywords =
-    orange3 add-on,ewoks
-
-[options]
-package_dir=
-	=src
-packages=find_namespace:
-python_requires = >=3.8
-install_requires =
-    numpy
-    scipy
-    h5py >=3.1,<3.10
-    silx >=0.15
-    Pint
-    ewoks[orange] >=0.1
-    ewoksorange >= 0.7.0rc0
-
-[options.packages.find]
-where=src
-
-[options.entry_points]
-console_scripts =
-    est=est.__main__:main
-orange3.addon =
-    est-add-on=orangecontrib.est
-orange.widgets =
-    Est=orangecontrib.est.widgets
-orange.widgets.tutorials =
-    Est=est.resources.workflows
-orange.canvas.help =
-    html-index=orangecontrib.est.widgets:WIDGET_HELP_PATH
-ewoks.tasks.class =
-    est.core.process.*=est1
-    est.core.process.*.*=est2
-
-[options.package_data]
-* = *.ows, *.png, *.svg, *.dat, *.xmu, *.ipynb
-
-[options.extras_require]
-pymca =
-    pymca >=5.8.1
-larch =
-    xraylarch >=0.9.71
-orange =
-    Orange3
-full =
-    %(pymca)s
-    %(larch)s
-    %(orange)s
-test_no_larh_or_pymca =
-    pytest >=7
-    testbook
-    ipykernel
-    pyqt5
-test =
-    %(full)s
-    %(test_no_larh_or_pymca)s
-dev =
-    %(test)s
-    black >=22
-    flake8 >=4
-    flake8_nb >= 0.3.1
-    pillow >= 10.0
-doc =
-    %(test)s
-    %(full)s
-    sphinx >=4.5
-    sphinx-autodoc-typehints >=1.16
-    ipykernel
-    nbsphinx
-    nbsphinx_link
-    pydata_sphinx_theme < 0.15
-
-# E501 (line too long) ignored for now
-# E203 and W503 incompatible with black formatting (https://black.readthedocs.io/en/stable/compatible_configs.html#flake8)
-[flake8]
-ignore = E501, E203, W503
-max-line-length = 88
-exclude =
-    .eggs
-
-# E402 (module import not at top of file) ignored
-[flake8_nb]
-ignore = E501, E203, W503, E402
-max-line-length = 88
-
-[coverage:run]
-omit =
-    */tests/*

setup.py

-import setuptools
-
-if __name__ == "__main__":
-    setuptools.setup()

src/est/__init__.py

-__version__ = "0.6.0"

src/est/__main__.py

@@ -8,7 +8,7 @@ Your environment should provide a command `est`. You can reach help with
 import logging
 import sys
 from silx.utils.launcher import Launcher
-from est import __version__
+from importlib.metadata import version as get_version
 
 
 def main():
@@ -20,7 +20,8 @@ def main():
     :rtype: int
     :returns: The execution status
     """
-    launcher = Launcher(prog="est", version=__version__)
+    est_version = get_version("est")
+    launcher = Launcher(prog="est", version=est_version)
     launcher.add_command(
         "canvas",
         module_name="ewoksorange.canvas.main",

src/est/core/io.py

@@ -8,7 +8,9 @@ from silx.io.url import DataUrl
 
 from est.units import ur
 from est import settings
-from est.io import read_xas, write_xas
+from est.io import read_xas
+from est.io import write_xas
+from est.io.concatenated import read_concatenated_xas
 from est.core.types import XASObject
 from est.core.types import dimensions as dimensions_mod
 from est.io.information import InputInformation
@@ -27,7 +29,10 @@ DEFAULT_CONF_PATH = "/configuration"
 def read_from_input_information(
     information: InputInformation, timeout: float = settings.DEFAULT_READ_TIMEOUT
 ) -> XASObject:
-    spectra, energy, configuration = read_xas(information=information, timeout=timeout)
+    if information.is_concatenated:
+        spectra, energy, configuration = read_concatenated_xas(information, timeout)
+    else:
+        spectra, energy, configuration = read_xas(information, timeout)
 
     xas_obj = XASObject(spectra=spectra, energy=energy, configuration=configuration)
     I0_url = information.I0_url
@@ -59,6 +64,10 @@ def read_from_url(
     I1_url: DataUrl | None = None,
     I2_url: DataUrl | None = None,
     mu_ref_url: DataUrl | None = None,
+    is_concatenated: bool = False,
+    trim_concatenated_n_points: int = 0,
+    skip_concatenated_n_spectra: int = 0,
+    concatenated_spectra_section_size: int = 0,
     timeout: float = settings.DEFAULT_READ_TIMEOUT,
 ) -> XASObject:
     """
@@ -83,6 +92,10 @@ def read_from_url(
         I1_url=I1_url,
         I2_url=I2_url,
         mu_ref_url=mu_ref_url,
+        is_concatenated=is_concatenated,
+        trim_concatenated_n_points=trim_concatenated_n_points,
+        skip_concatenated_n_spectra=skip_concatenated_n_spectra,
+        concatenated_spectra_section_size=concatenated_spectra_section_size,
     )
     return read_from_input_information(input_information, timeout=timeout)
 
@@ -129,6 +142,8 @@ def dump_xas(h5_file: str, xas_obj: Union[dict, XASObject]) -> None:
     """
     if isinstance(xas_obj, dict):
         xas_obj = XASObject.from_dict(xas_obj)
+    if not isinstance(xas_obj, XASObject):
+        raise TypeError(str(type(xas_obj)))
 
     if not h5_file:
         _logger.warning("no output file defined, please give path to the output file")

src/est/core/monotonic.py

+from typing import Sequence, List, Tuple
+
+import numpy
+
+
+def split_piecewise_monotonic(values: Sequence[float]) -> List[slice]:
+    """This method returns the disjoint slices representing monotonic sections.
+
+    The provided values are assumed to be piecewise monotonic which means that
+    it consists of sections that are either monotonically increasing (∀ i ≤ j, x[i] ≤ x[j])
+    or monotonically decreasing (∀ i ≤ j, x[i] ≥ x[j]). Note that a list of identical
+    values is both monotonically increasing and decreasing.
+    """
+    section_sizes = []
+    section_slopes = []
+    values_left = values
+    while len(values_left):
+        section_size, section_slope = _first_monotonic_size(values_left)
+        section_sizes.append(section_size)
+        section_slopes.append(section_slope)
+        values_left = values_left[section_size:]
+
+    monotone_start = [0]
+    monotone_stop = []
+    monotone_step = []
+    last_section_index = len(section_sizes) - 1
+    stops = numpy.cumsum(section_sizes)
+    for section_index, (stop, section_slope) in enumerate(zip(stops, section_slopes)):
+        monotone_step.append(1 if section_slope >= 0 else -1)
+
+        if section_index == last_section_index:
+            monotone_stop.append(stop)
+            break
+
+        # The pivot index is the index at which either
+        #  - slope>=0 with the previous index and slope<0 with the next index
+        #  - slope<=0 with the previous index and slope>0 with the next index
+        pivot_index = stop - 1
+
+        if values[pivot_index - 1] == values[pivot_index]:
+            # The pivot index ■ is part of the next section
+            #
+            #    ● ─ ■
+            #   /     \     -> same slope up and down
+            #  ●       ●
+            #
+            monotone_stop.append(stop - 1)
+            monotone_start.append(stop - 1)
+            continue
+
+        # Determine whether the pivot index is part of this section or
+        # be part of the next section
+        slope_before = values[pivot_index] - values[pivot_index - 1]
+        diff_slope_before = abs(section_slope - slope_before)
+
+        slope_after = values[pivot_index + 1] - values[pivot_index]
+        next_section_slope = section_slopes[section_index + 1]
+        diff_slope_after = abs(next_section_slope - slope_after)
+
+        if diff_slope_after <= diff_slope_before:
+            # The pivot index ■ is part of the next section
+            #
+            #       ■
+            #    ●   \       -> slope after matches the next section slope better
+            #   /     ●         then the slope before matches the current section slope
+            #  ●       \
+            # /         ●
+            #
+            monotone_stop.append(stop - 1)
+            monotone_start.append(stop - 1)
+        else:
+            # The pivot index ■ is part of this section
+            #
+            #     ■
+            #    /   ●      -> slope before matches the current section slope better
+            #   ●     \        than the slope after matches the next section slope
+            #  /       ●
+            # ●         \
+            #
+            monotone_stop.append(stop)
+            monotone_start.append(stop)
+
+    return [
+        _create_slice(start, stop, step)
+        for start, stop, step in zip(monotone_start, monotone_stop, monotone_step)
+    ]
+
+
+def _create_slice(start: int, stop: int, step: int):
+    if step >= 0:
+        return slice(start, stop, step)
+    assert start >= 0
+    assert stop >= 0
+    start, stop = stop, start
+    start -= 1
+    if stop == 0:
+        stop = None
+    else:
+        stop -= 1
+    return slice(start, stop, step)
+
+
+def _mean_nonzero(values: Sequence[float]) -> float:
+    """Average non-zero value. Returns `nan` for an empty list and `0.` when
+    all values are zero.
+    """
+    values = numpy.asarray(values)
+    if not values.size:
+        return numpy.nan
+    non_zero = values != 0
+    if non_zero.any():
+        return numpy.mean(values[non_zero])
+    return 0.0
+
+
+def _first_monotonic_size(values: Sequence[float]) -> Tuple[int, int]:
+    """Determine the length of the first monotonically increasing or decreasing slice
+    starting from the first value.
+    """
+    slopes = numpy.diff(values)
+
+    maxsize = len(values)
+    if maxsize < 3:
+        return maxsize, _mean_nonzero(slopes)
+
+    slope_signs = numpy.sign(slopes)
+    first_slope_sign = slope_signs[0]
+    for value_idx, slope_sign in enumerate(slope_signs[1:], 1):
+        if slope_sign and first_slope_sign and slope_sign != first_slope_sign:
+            # Non-zero slope changed sign: end of monotonic series
+            return value_idx + 1, _mean_nonzero(slopes[:value_idx])
+        if not first_slope_sign:
+            first_slope_sign = slope_sign
+
+    return maxsize, _mean_nonzero(slopes)

src/est/core/process/energyroi.py

 """contains `energy roi` related functions / classes"""
 
+from typing import Union, Optional
+
 from est.core.types.xasobject import XASObject
 from .process import Process
 
 
-def xas_energy_roi(xas_obj):
-    """
-    apply roi on the XASObject.spectra
-
-    :param xas_obj: object containing the configuration and spectra to process
-    :type: Union[:class:`.XASObject`, dict]
-    :return: spectra dict
-    :rtype: :class:`.XASObject`
-    """
+def xas_energy_roi(xas_obj: Union[XASObject, dict]) -> Optional[XASObject]:
     process = EnergyROIProcess(inputs={"xas_obj": xas_obj})
     process.run()
     return process.get_output_value("xas_obj", None)
@@ -20,37 +14,27 @@ def xas_energy_roi(xas_obj):
 
 class EnergyROIProcess(
     Process,
-    name="energy roi",
     input_names=["xas_obj"],
     optional_input_names=["energy_roi"],
     output_names=["xas_obj"],
 ):
     @staticmethod
-    def program_name():
+    def program_name() -> str:
         return "energy-roi"
 
-    def definition(self):
+    def definition(self) -> str:
         return "apply a ROI on energy range"
 
     def run(self):
-        """
-
-        :param xas_obj: object containing the configuration and spectra to process
-        :type: Union[:class:`.XASObject`, dict]
-        :return: spectra dict
-        :rtype: :class:`.XASObject`
-        """
-        xas_obj = self.inputs.xas_obj
-        _xas_obj = self.getXasObject(xas_obj=xas_obj)
-        assert isinstance(_xas_obj, XASObject)
+        xas_obj = self.getXasObject(xas_obj=self.inputs.xas_obj)
 
         energy_roi = self.get_input_value("energy_roi", dict())
 
         self.progress = 0.0
-        self._apply_roi(_xas_obj, energy_roi.get("minE"), energy_roi.get("maxE"))
+        self._apply_roi(xas_obj, energy_roi.get("minE"), energy_roi.get("maxE"))
         self.progress = 100.0
 
-        self.outputs.xas_obj = _xas_obj
+        self.outputs.xas_obj = xas_obj
 
     def _apply_roi(self, xas_obj, emin, emax):
         if emin is None and emax is None:

src/est/core/process/handle_nan.py

+import numpy
+
+
+def array_undo_mask(masked: numpy.ndarray, mask: numpy.ndarray) -> numpy.ndarray:
+    """
+    Restore an array to its original shape after applying a boolean mask.
+
+    :param masked: The array containing only the unmasked values.
+    :param mask: A boolean array indicating the original positions of the `masked` values.
+    :return: A reconstructed array of the same shape as `mask`, where values from `masked`
+             are restored to their original positions, and other elements are filled
+             with `NaN` (for floats) or `0` (for ints).
+
+    **Example:**
+
+    >>> import numpy as np
+    >>> original = np.array([1.0, 2.0, np.nan, 4.0, np.nan])
+    >>> mask = ~np.isnan(original)  # Boolean mask
+    >>> masked = original[mask]     # Extract non-NaN values
+    >>> restored = array_undo_mask(masked, mask)
+    >>> print(restored)
+    [ 1.  2. nan  4. nan ]
+    """
+    if not mask.any():
+        return masked
+    if numpy.issubdtype(masked.dtype, int):
+        raise TypeError("Integers are not supported")
+    result = numpy.full(mask.shape, numpy.nan, dtype=masked.dtype)
+    result[mask] = masked
+    return result