MiraGeoscience · MatthieuCMira · Dec 2, 2025 · Dec 2, 2025
diff --git a/docs/peak_finder_app/Makefile b/docs/peak_finder_app/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/peak_finder_app/environnment.yml b/docs/peak_finder_app/environnment.yml
@@ -0,0 +1,18 @@
+name: gempy-drivers-docs
+
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.10
+  - pip
+  - pip:
+    - sphinx
+    - sphinx_issues
+    - sphinx_rtd_theme
+    - sphinxcontrib-bibtex
+    - sphinxcontrib-googleanalytics
+    - numpydoc
+    - geoh5py
+    - geoapps-utils
+    - curve-apps
diff --git a/docs/peak_finder_app/make.bat b/docs/peak_finder_app/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/peak_finder_app/source/THIRD_PARTY_SOFTWARE.rst b/docs/peak_finder_app/source/THIRD_PARTY_SOFTWARE.rst
@@ -0,0 +1,47 @@
+Third Party Software
+====================
+
+The Peak-Finder repository and source distributions bundle several libraries that are
+compatibly licensed.  We list these here.
+
+
+.. list-table::
+  :widths: 30 30 60
+  :header-rows: 1
+
+  * - Name
+    - License
+    - Description
+  * - `curve-apps <https://github.com/MiraGeoscience/curve-apps>`_
+    - MIT
+    - Application for the creation of geoh5 Curves object from data.
+  * - `Dask <https://github.com/dask/dask/>`_
+    - BSD-3-Clause
+    - Parallel PyData with Task Scheduling
+  * - `dash-daq <https://github.com/plotly/dash-daq>`_
+    - MIT
+    - DAQ components for Dash
+  * - `geoapps-utils <https://github.com/MiraGeoscience/geoapps-utils>`_
+    - MIT
+    - Collection of utilities for creating applications and manipulating geoh5 objects.
+  * - `geoh5py <https://github.com/MiraGeoscience/geoh5py>`_
+    - LGPL-3.0-or-later
+    - Python API for geoh5, an open file format for geoscientific data
+  * - `libhwloc <https://github.com/conda-forge/libhwloc-feedstock>`_
+    - BSD-3-Clause
+    - Portable Hardware Locality (hwloc)
+  * - `numpy <https://github.com/numpy/numpy>`_
+    - BSD-3-Clause
+    - Fundamental package for array computing in Python
+  * - `plotly <https://github.com/plotly/plotly.py>`_
+    - MIT
+    - An open-source, interactive data visualization library for Python
+  * - `pyside <https://wiki.qt.io/Qt_for_Python>`_
+    - LGPL
+    - Python bindings for the Qt cross-platform application and UI framework
+  * - `scipy <https://github.com/scipy/scipy>`_
+    - BSD-3-Clause
+    - Fundamental algorithms for scientific computing in Python
+  * - `tqdm <https://github.com/tqdm>`_
+    - MPL-2.0 or MIT
+    - A Fast, Extensible Progress Bar for Python and CLI
diff --git a/docs/peak_finder_app/source/conf.py b/docs/peak_finder_app/source/conf.py
@@ -0,0 +1,74 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+from datetime import datetime
+from importlib.metadata import version
+
+from packaging.version import Version
+
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "peak-finder"
+
+# The full version, including alpha/beta/rc tags.
+release = version("peak-finder-app")
+# The short X.Y.Z version.
+version = Version(release).base_version
+
+project_copyright = "%Y, Mira Geoscience Ltd"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+autodoc_mock_imports = [
+    "curve_apps",
+    "dash",
+    "dask",
+    "flask",
+    "geoapps_utils",
+    "geoh5py",
+    "numpy",
+    "plotly",
+    "pyqtwebengine",
+    "pyside2",
+    "scipy",
+    "tqdm",
+]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.todo",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+todo_include_todos = True
+
+# -- Options for auto-doc ----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#module-sphinx.ext.autodoc
+
+autodoc_typehints = "signature"
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "alabaster"
+html_theme_options = {
+    "description": f"version {release}",
+}
+
+# Enable numref
+numfig = True
+
+
+def get_copyright_notice():
+    return f"Copyright {datetime.now().strftime(project_copyright)}"
+
+
+rst_epilog = f"""
+.. |copyright_notice| replace:: {get_copyright_notice()}.
+"""
diff --git a/docs/peak_finder_app/source/getting_started.rst b/docs/peak_finder_app/source/getting_started.rst
@@ -0,0 +1,112 @@
+.. _getting_started:
+
+Getting Started
+===============
+
+Whether you are a developer or an end-user, this page will help you get started with the **peak-finder**.
+
+Installation
+------------
+
+Install Conda
+~~~~~~~~~~~~~
+
+Install Conda for Python 3.10 or higher. Follow this link to download its Windows installer (~140 MB of disk space):
+
+`Miniforge <https://github.com/conda-forge/miniforge#download>`_ `(Windows x86_64) <https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Windows-x86_64.exe>`_
+
+.. figure:: /images/getting_started/Miniforge3_Setup-1.png
+    :align: center
+    :width: 200
+
+.. figure:: /images/getting_started/Miniforge3_Setup-3.png
+    :align: center
+    :width: 200
+
+Registering the Conda distribution as the default Python 3.10 interpreter is optional.
+Preferably uncheck that box if you already have Python 3 installed on your system.
+
+.. note:: We recommend installing **Miniforge**: beyond being smaller,
+    it also installs packages from the conda-forge repository by default,
+    which has no restriction for commercial use, while both Miniconda and Anaconda distributions use
+    the Anaconda repository by default: see `Anaconda Terms of Service <https://www.anaconda.com/terms-of-service>`_ for details.
+    In any case, the installation of **peak-finder** forces the usage of the conda-forge repository,
+    and is thus not affected by the Anaconda Terms of Service.
+
+Download the latest peak-finder
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Follow this link to `download from the GitHub repository <https://github.com/MiraGeoscience/peak-finder-app/archive/refs/heads/main.zip>`_.
+
+Extract the package to your drive (SSD if available)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Extract the package to your drive, preferably an SSD if available.
+
+.. figure:: /images/getting_started/extract.png
+    :align: center
+    :width: 50%
+
+
+Run ``Install_or_Update.bat``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The same batch file can be used to install or update **peak-finder**.
+A conda environment named ``peak-finder`` will be created to prevent conflicts with other software that may rely on Python.
+
+.. figure:: /images/getting_started/install_or_update.png
+    :align: center
+    :width: 50%
+
+.. note:: The assumption is made that Conda has been installed in one
+   of the default directories, depending on the distribution
+   (miniforge3, mambaforge, miniconda3, anaconda3):
+
+   - %LOCALAPPDATA%\\
+   - %USERPROFILE%\\
+   - %LOCALAPPDATA%\\Continuum\\
+   - %PROGRAMDATA%\\
+
+If Conda gets installed in a different directory, users will need to add/edit a
+``get_custom_conda.bat`` file to add their custom path to the ``conda.bat`` file:
+
+.. figure:: /images/getting_started/Install_start_bat.png
+    :align: center
+    :width: 75%
+
+
+Running the application
+-----------------------
+At this point, you will have all required packages to run the applications.
+Geoscience ANALYST pro users can run the application with a **ui.json** file
+by drag-and-drop:
+
+.. figure:: /images/getting_started/drag_and_drop.png
+    :align: center
+    :width: 75%
+
+or by Python menu dropdown by placing a **ui.json** file
+in the Python scripts folder.
+
+**1.**
+
+.. figure:: /images/getting_started/python_scripts_folder.png
+    :align: center
+    :width: 75%
+
+**2.**
+
+.. figure:: /images/getting_started/python_menu_uijson.png
+    :align: center
+    :width: 75%
+
+**3.**
+
+.. figure:: /images/getting_started/dropdown_scripts.png
+    :align: center
+    :width: 75%
+
+Either operation will result in the rendering of a ui.json file within the
+Geoscience ANALYST viewport.  To learn about the ui.json interface and how
+to run the application in one of two modes, proceed to the
+:ref:`Basic Usage <usage>` section.
diff --git a/docs/peak_finder_app/source/images/getting_started/Install_start_bat.png b/docs/peak_finder_app/source/images/getting_started/Install_start_bat.png
diff --git a/docs/peak_finder_app/source/images/getting_started/Miniforge3_Setup-1.png b/docs/peak_finder_app/source/images/getting_started/Miniforge3_Setup-1.png
diff --git a/docs/peak_finder_app/source/images/getting_started/Miniforge3_Setup-3.png b/docs/peak_finder_app/source/images/getting_started/Miniforge3_Setup-3.png
diff --git a/docs/peak_finder_app/source/images/getting_started/drag_and_drop.png b/docs/peak_finder_app/source/images/getting_started/drag_and_drop.png
diff --git a/docs/peak_finder_app/source/images/getting_started/dropdown_scripts.png b/docs/peak_finder_app/source/images/getting_started/dropdown_scripts.png
diff --git a/docs/peak_finder_app/source/images/getting_started/extract.png b/docs/peak_finder_app/source/images/getting_started/extract.png
diff --git a/docs/peak_finder_app/source/images/getting_started/install_or_update.png b/docs/peak_finder_app/source/images/getting_started/install_or_update.png
diff --git a/docs/peak_finder_app/source/images/getting_started/python_menu_uijson.png b/docs/peak_finder_app/source/images/getting_started/python_menu_uijson.png
diff --git a/docs/peak_finder_app/source/images/getting_started/python_scripts_folder.png b/docs/peak_finder_app/source/images/getting_started/python_scripts_folder.png
diff --git a/docs/peak_finder_app/source/images/getting_started/uijson_parameters.png b/docs/peak_finder_app/source/images/getting_started/uijson_parameters.png
diff --git a/docs/peak_finder_app/source/images/getting_started/using_interface.png b/docs/peak_finder_app/source/images/getting_started/using_interface.png
diff --git a/docs/peak_finder_app/source/images/interactive/ui_controls.png b/docs/peak_finder_app/source/images/interactive/ui_controls.png
diff --git a/docs/peak_finder_app/source/images/interactive/visualizations.png b/docs/peak_finder_app/source/images/interactive/visualizations.png
diff --git a/docs/peak_finder_app/source/images/introduction/app_overview.png b/docs/peak_finder_app/source/images/introduction/app_overview.png
diff --git a/docs/peak_finder_app/source/images/methodology/merge_peaks.png b/docs/peak_finder_app/source/images/methodology/merge_peaks.png
diff --git a/docs/peak_finder_app/source/images/methodology/min_amplitude.png b/docs/peak_finder_app/source/images/methodology/min_amplitude.png
diff --git a/docs/peak_finder_app/source/images/methodology/min_value.png b/docs/peak_finder_app/source/images/methodology/min_value.png
diff --git a/docs/peak_finder_app/source/images/methodology/min_width.png b/docs/peak_finder_app/source/images/methodology/min_width.png
diff --git a/docs/peak_finder_app/source/images/methodology/peak_finder_params.png b/docs/peak_finder_app/source/images/methodology/peak_finder_params.png
diff --git a/docs/peak_finder_app/source/images/parameters/data_selection/flip_y.png b/docs/peak_finder_app/source/images/parameters/data_selection/flip_y.png
diff --git a/docs/peak_finder_app/source/images/parameters/data_selection/group_colors.png b/docs/peak_finder_app/source/images/parameters/data_selection/group_colors.png
diff --git a/docs/peak_finder_app/source/images/parameters/data_selection/lines.png b/docs/peak_finder_app/source/images/parameters/data_selection/lines.png
diff --git a/docs/peak_finder_app/source/images/parameters/data_selection/masking_data.png b/docs/peak_finder_app/source/images/parameters/data_selection/masking_data.png
diff --git a/...eak_finder_app/source/images/parameters/data_selection/outward_line_compare.png b/...eak_finder_app/source/images/parameters/data_selection/outward_line_compare.png
diff --git a/docs/peak_finder_app/source/images/parameters/data_selection/outward_lines.png b/docs/peak_finder_app/source/images/parameters/data_selection/outward_lines.png
diff --git a/docs/peak_finder_app/source/images/parameters/data_selection/select_line.png b/docs/peak_finder_app/source/images/parameters/data_selection/select_line.png
diff --git a/docs/peak_finder_app/source/images/parameters/data_selection_parameters.png b/docs/peak_finder_app/source/images/parameters/data_selection_parameters.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/export.png b/docs/peak_finder_app/source/images/parameters/detection/export.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/group_separation.png b/docs/peak_finder_app/source/images/parameters/detection/group_separation.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/live_link.png b/docs/peak_finder_app/source/images/parameters/detection/live_link.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/max_migration.png b/docs/peak_finder_app/source/images/parameters/detection/max_migration.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/merge_peaks.png b/docs/peak_finder_app/source/images/parameters/detection/merge_peaks.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/minimum_amplitude.png b/docs/peak_finder_app/source/images/parameters/detection/minimum_amplitude.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/minimum_channels.png b/docs/peak_finder_app/source/images/parameters/detection/minimum_channels.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/minimum_data.png b/docs/peak_finder_app/source/images/parameters/detection/minimum_data.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/minimum_width.png b/docs/peak_finder_app/source/images/parameters/detection/minimum_width.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/output_path.png b/docs/peak_finder_app/source/images/parameters/detection/output_path.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/save_as.png b/docs/peak_finder_app/source/images/parameters/detection/save_as.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection/smoothing.png b/docs/peak_finder_app/source/images/parameters/detection/smoothing.png
diff --git a/docs/peak_finder_app/source/images/parameters/detection_parameters.png b/docs/peak_finder_app/source/images/parameters/detection_parameters.png
diff --git a/docs/peak_finder_app/source/images/parameters/visual_parameters.png b/docs/peak_finder_app/source/images/parameters/visual_parameters.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/linear_threshold.png b/docs/peak_finder_app/source/images/parameters/visualization/linear_threshold.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/linthresh10e-3p2.png b/docs/peak_finder_app/source/images/parameters/visualization/linthresh10e-3p2.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/linthresh10e-5p1.png b/docs/peak_finder_app/source/images/parameters/visualization/linthresh10e-5p1.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/linthresh_compare.png b/docs/peak_finder_app/source/images/parameters/visualization/linthresh_compare.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/markers.png b/docs/peak_finder_app/source/images/parameters/visualization/markers.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/outward_lines_1.png b/docs/peak_finder_app/source/images/parameters/visualization/outward_lines_1.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/plot_markers.png b/docs/peak_finder_app/source/images/parameters/visualization/plot_markers.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/plot_residuals.png b/docs/peak_finder_app/source/images/parameters/visualization/plot_residuals.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/residuals.png b/docs/peak_finder_app/source/images/parameters/visualization/residuals.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/section_xlabel.png b/docs/peak_finder_app/source/images/parameters/visualization/section_xlabel.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/trend_lines.png b/docs/peak_finder_app/source/images/parameters/visualization/trend_lines.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/xlabel.png b/docs/peak_finder_app/source/images/parameters/visualization/xlabel.png
diff --git a/docs/peak_finder_app/source/images/parameters/visualization/yscale.png b/docs/peak_finder_app/source/images/parameters/visualization/yscale.png
diff --git a/docs/peak_finder_app/source/images/standalone/ui.png b/docs/peak_finder_app/source/images/standalone/ui.png
diff --git a/docs/peak_finder_app/source/images/usage/general_parameters.png b/docs/peak_finder_app/source/images/usage/general_parameters.png
diff --git a/docs/peak_finder_app/source/images/usage/groups.png b/docs/peak_finder_app/source/images/usage/groups.png
diff --git a/docs/peak_finder_app/source/images/usage/optional_parameters.png b/docs/peak_finder_app/source/images/usage/optional_parameters.png
diff --git a/docs/peak_finder_app/source/images/usage/xlabel.png b/docs/peak_finder_app/source/images/usage/xlabel.png
diff --git a/docs/peak_finder_app/source/index.rst b/docs/peak_finder_app/source/index.rst
@@ -0,0 +1,74 @@
+About
+=====
+
+Peak-finder has been designed for the detection and grouping of time-domain
+electromagnetic (TEM) anomalies measured along flight lines. Anomaly markers
+can be exported to `Geoscience ANALYST <https://www.mirageoscience.com/mining-industry-software/geoscience-analyst/>`_,
+along with various metrics for characterization and targeting.
+
+.. figure:: /images/interactive/visualizations.png
+
+The peak-finder application can operate in two modes:
+
+ - :ref:`Interactive <interactive_application>` (shown above)
+ - :ref:`Standalone <standalone_application>`
+
+While initially designed for TEM data, the same application can be used for
+characterization of anomalies of mixed data types (eg. magnetics, gravity,
+topography, etc..).
+
+.. toctree::
+   :maxdepth: 1
+
+   getting_started
+   usage
+   methodology
+   interactive_application
+   standalone_application
+   THIRD_PARTY_SOFTWARE
+
+
+New user?
+---------
+
+Visit the :ref:`getting_started` page.
+
+
+License
+^^^^^^^
+MIT License
+
+Copyright (c) 2023-2025 Mira Geoscience
+
+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.
+
+Third Party Software
+^^^^^^^^^^^^^^^^^^^^
+The octree-creation-app Software may provide links to third party libraries or code (collectively “Third Party Software”)
+to implement various functions. Third Party Software does not comprise part of the Software.
+The use of Third Party Software is governed by the terms of such software license(s).
+Third Party Software notices and/or additional terms and conditions are located in the
+`THIRD_PARTY_SOFTWARE.rst`_ file.
+
+.. _THIRD_PARTY_SOFTWARE.rst: THIRD_PARTY_SOFTWARE.rst
+
+
+Copyright
+^^^^^^^^^
+|copyright_notice|