deploy: cf0c5b5

.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 1d08db85a79bfccf7301ffbec52d7ebe
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/coordination_api.rst.txt

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+
+coordination
+============
+
+(WIP)

_sources/export_api.rst.txt

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+
+export
+======
+
+(WIP)

_sources/filter_im_api.rst.txt

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+
+**filter_im**
+=============
+
+The ``filter_im`` module contains functions that pre-process XCT images like segmentation and cropping, allowing for 
+pore structure analysis. This is mainly used as a quick method of processing raw XCT scans, but Pore2Chip operates 
+best on already segmented data, as the methods of segmentation used here rely on Otsu's filtering, which may not capture 
+solid matter of a particular density (ex. plant roots).
+
+----
+
+filter_single()
+---------------
+
+.. autofunction:: pore2chip.filter_im.filter_single
+
+..
+
+    The coordinates for cropx and cropy begin at the top left.
+
+----
+
+filter_list()
+-------------
+
+.. autofunction:: pore2chip.filter_im.filter_list
+
+..
+
+    The coordinates for cropx and cropy begin at the top left.
+
+----
+
+read_and_filter()
+-----------------
+
+.. autofunction:: pore2chip.filter_im.read_and_filter
+
+..
+
+    The coordinates for cropx and cropy begin at the top left.
+
+----
+
+read_and_filter_list()
+----------------------
+
+.. autofunction:: pore2chip.filter_im.read_and_filter_list
+
+..
+
+    The coordinates for cropx and cropy begin at the top left.
+
+    Leave crop_depth empty to include all files in directory.
+
+.. note::
+
+   This project is under active development.

_sources/generate_api.rst.txt

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+
+generate
+========
+
+(WIP)

_sources/index.rst.txt

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+.. Pore2Chip documentation master file, created by
+   sphinx-quickstart on Thu Jan  2 09:45:53 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Pore2Chip Documentation
+=======================
+A python package that takes XCT images of porous materials and generates representative digital twin micromodels.
+
+.. figure:: _static/ModEx_Loop_SoilChip.jpg
+   :width: 636px
+   :height: 453px
+   :scale: 100 %
+   :alt: ModEx Loop for Pore2Chip and Chip2Flow
+
+ModEx Loop for Pore2Chip and Chip2Flow
+
+About Pore2Chip
+---------------
+**Pore2Chip** is a Python module designed to streamline the process of analyzing X-ray computed tomography (XCT) 
+images of soil and creating 2D micromodel designs based on that analysis. 
+It leverages the power of open-source libraries like OpenPNM, PoreSpy, and drawsvg to extract key information about the soil's 
+porous structure and translate it into a blueprint for microfluidic simulations or physical "lab-on-a-chip" devices developed using additive manufacturing.
+
+User Guide
+----------
+.. toctree::
+   :maxdepth: 1
+
+   install
+   quickstart
+   module_ref
+
+Acknowledgements
+----------------
+This research was performed on a project award (Award DOIs: 10.46936/ltds.proj.2024.61069/60012423; 10.46936/intm.proj.2023.60674/60008777; 10.46936/intm.proj.2023.60904/60008965) 
+from the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program under contract no. DE-AC05-76RL01830. 
+The authors acknowledge the contributions of Michael Perkins at PNNL’s Creative Services, who developed the conceptual graphics in this paper.
+
+PNNL-SA-197910
+
+Disclaimer
+----------
+This research work was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, 
+nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, 
+apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, 
+or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. 
+The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.
+
+.. note::
+
+   This project is under active development.
+
+

_sources/install.rst.txt

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+
+.. Installation
+.. =======================
+
+.. The OpenPNM and PoreSpy libraries are required to analyze XCT images. PoreSpy is used to generate a 
+.. pore network that is used to extract pore size distribution, pore throat size distribution, and pore coordination numbers. 
+.. OpenPNM is used to construct a new 2D pore network that will be used to create the micromodel design.
+
+.. Install using PiP:
+
+.. .. code-block:: console
+        .. $ pip install pore2chip
+
+Installation
+============
+
+The OpenPNM and PoreSpy libraries are required to analyze XCT images. PoreSpy is used to generate a 
+pore network that is used to extract pore size distribution, pore throat size distribution, and pore coordination numbers. 
+OpenPNM is used to construct a new 2D pore network that will be used to create the micromodel design.
+
+Pip Installation
+----------------
+Install using PiP:
+
+.. code-block:: bash
+
+   pip install pore2chip
+
+Install from source:
+
+.. code-block:: bash
+
+   git clone https://github.com/EMSL-Computing/Pore2Chip.git 
+   cd Pore2Chip
+   python3 -m build
+   python3 -m pip install pore2chip --no-index --find-links dist/
+
+Conda Environment
+-----------------
+Creating a Conda environment:
+
+.. code-block:: bash
+
+   conda create -n pore2chip python=3.9
+   conda activate pore2chip
+   pip install pore2chip
+
+Docker Image
+------------
+Building a Docker Image with Jupyter Notebook:
+
+.. code-block:: bash
+
+   git clone https://github.com/EMSL-Computing/Pore2Chip.git 
+   cd Pore2Chip
+   docker build -t pore2chip
+   docker run -p 8888:8888 pore2chip
+
+This will automatically run a Jupyter Notebook server in the browser with a python environment that 
+has Pore2Chip and all of its dependencies installed.
+
+.. note::
+
+   This project is under active development.

_sources/io_api.rst.txt

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+
+io
+==
+
+(WIP)

_sources/metrics_api.rst.txt

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+
+**metrics**
+===========
+
+The ``metrics`` module contains functions that extract pore data from segmented images.
+
+----
+
+feret_diameter()
+----------------
+
+.. autofunction:: pore2chip.metrics.feret_diameter
+
+----
+
+feret_diameter_list()
+---------------------
+
+.. autofunction:: pore2chip.metrics.feret_diameter_list
+
+----
+
+extract_diameters()
+-------------------
+
+.. autofunction:: pore2chip.metrics.extract_diameters
+
+----
+
+extract_diameters2()
+--------------------
+
+.. autofunction:: pore2chip.metrics.extract_diameters2
+
+----
+
+extract_diameters_alt()
+-----------------------
+
+.. autofunction:: pore2chip.metrics.extract_diameters_alt
+
+----
+
+get_probability_density()
+-------------------------
+
+.. autofunction:: pore2chip.metrics.get_probability_density
+
+----
+
+get_percent_probability()
+-------------------------
+
+.. autofunction:: pore2chip.metrics.get_percent_probability
+
+
+.. note::
+
+   This project is under active development.

_sources/module_ref.rst.txt

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+
+Module Reference
+================
+
+Here are the references for all Pore2Chip's modules:
+
+.. toctree::
+   :maxdepth: 2
+
+   filter_im_api
+   metrics_api
+   coordination_api
+   generate_api
+   export_api
+   io_api