Merge pull request #12 from PermafrostDiscoveryGateway/develop

Release 0.0.2 of LiDAR tiling workflow

.gitignore

@@ -1,3 +1,9 @@
+# Test artifacts
+pdgpoints/testdata/lp_jumps.laz
+pdgpoints/testdata/tileset.json
+pdgpoints/testdata/*[.txt|.zip]
+pdgpoints/testdata/*/
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

MANIFEST.in

@@ -0,0 +1,3 @@
+include pdgpoints/bin/*
+include pdgpoints/testdata/*
+include pdgpoints/log/*

README.md

@@ -1,2 +1,139 @@
 # viz-points
-Pythonpackage for post-processing point-cloud data for 3D visualization
+Python package for post-processing point-cloud data for 3D visualization
+
+## Repository contents
+
+- [notebooks/](notebooks/) contains the simplified and annotated Jupyter Notebook version of the LiDAR processing workflow
+- [pdgpoints/](pdgpoints/) contains the application code comprising the library
+
+## Installation
+
+### Hardware requirements
+This software requires an x86_64 architecture and a Linux environment.
+
+### Software requirements
+- [pdal](https://github.com/PDAL/python) (pip installation may not build...if so use [anaconda](https://anaconda.org/) or [miniconda](https://repo.anaconda.com/miniconda/))
+- [py3dtiles](https://gitlab.com/oslandia/py3dtiles) (Oslandia versions after [522ce61a](https://gitlab.com/Oslandia/py3dtiles/-/blob/522ce61a0c2cbeb496ba4862e14477bb941b23a3/py3dtiles/merger.py))
+- rapidlasso [las2las](https://rapidlasso.com/lastools/las2las/) and [lasinfo](https://rapidlasso.com/lastools/lasinfo/) post-November 2022 (rapidlasso [precompiled Windows](https://github.com/LAStools/LAStools/blob/master/README.md#links) or included [linux binary](https://rapidlasso.de/release-of-lastoolslinux/))
+
+Visualization requirements:
+- A tool that can display 3dtiles data, such as [Cesium](https://cesium.com)
+
+### Unix installation example
+
+Remember to set up and activate your virtual environment before proceeding.
+
+```bash
+# use conda to set up environment
+conda create -n viz-points python=3.9
+conda activate viz-points
+conda install -c conda-forge pdal
+# get and install this software
+git clone https://github.com/PermafrostDiscoveryGateway/viz-points.git
+cd viz-points
+# checkout the development branch if necessary
+git checkout develop
+pip install .
+# test your installation
+tilepoints-test
+```
+
+## Usage
+
+This software is designed to be used either as a command line tool or as a Python package.
+
+### Command line usage
+
+**Command syntax:**
+```
+tilepoints [ OPTIONS ] -f /path/to/file.las
+```
+
+**Required argument:**
+```
+    -f file.las | --file=/path/to/file.las
+            specify the path to a LAS or LAZ point cloud file
+```
+
+**Options:**
+```
+    -h | --help
+            display the help message
+    -v | --verbose
+            display more informational messages
+    -c | --copy_I_to_RGB
+            copy intensity values to RGB channels
+    -m | --merge
+            merge all tilesets in the output folder (./3dtiles)
+    -a | --archive
+            copy original LAS files to a ./archive folder
+    -s X | --rgb_scale=X
+            scale RGB values by X amount
+    -z X | --translate_z=X
+            translate Z (elevation) values by X amount
+```
+
+### Python usage
+
+**Python example:**
+```python
+from pdgpoints.pipeline import Pipeline
+
+p = Pipeline(f='/path/to/file.laz',
+             intensity_to_RGB=True,
+             merge=True,
+             archive=False,
+             rgb_scale=4.0,
+             translate_z=-8.3,
+             verbose=False)
+p.run()
+```
+
+### Visualizing the data in Cesium
+
+You can view the output tiles in a Cesium environment. For steps for how to visualize the tiles with a local Cesium instance, see the [documentation here in pdg-info](https://github.com/julietcohen/pdg-info/blob/main/05_displaying-the-tiles.md#option-1-run-cesium-locally).
+
+![Test dataset](pdgpoints/testdata/lp.png)
+
+More info on the above test dataset [here](pdgpoints/testdata/README.md).
+
+Below is an example of the `cesium.js` file that will display a 3dtiles tileset at `./3dtiles/tileset.json` (you will need your own access token):
+
+
+```javascript
+
+function start(){// Your access token can be found at: https://cesium.com/ion/tokens.
+
+  Cesium.Ion.defaultAccessToken = "YOUR-TOKEN-HERE"
+
+  const viewer = new Cesium.Viewer('cesiumContainer');
+
+  const imageryLayers = viewer.imageryLayers;
+
+  var tileset = new Cesium.Cesium3DTileset({
+    url: "3dtiles/tileset.json",
+    debugShowBoundingVolume: true,
+    debugShowContentBoundingVolume: false,
+    debugShowGeometricError: false,
+    debugWireframe: true
+  });
+
+  viewer.scene.primitives.add(tileset);
+
+  window.zoom_to_me = function(){
+    viewer.zoomTo(tileset);
+  }
+
+  tileset.readyPromise.then(zoom_to_me).otherwise(error => { console.log(error) });
+}
+
+start()
+```
+
+# Referencing this repository
+
+If you would like to cite this repository, we suggest using something like the following:
+
+```
+Ian M. Nesbitt, Robyn Thiessen-Bock, and Matthew B. Jones (NCEAS). viz-points: A Python package for post-processing point-cloud data for 3D visualization. https://github.com/PermafrostDiscoveryGateway/viz-points.
+```

docsrc/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+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
+
+github:
+	@make html
+	@cp -a _build/html/. ../docs
+
+# 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)

docsrc/conf.py

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+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+# sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('../'))
+from datetime import datetime
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'viz-points'
+copyright = '%s, National Center for Ecological Analysis and Synthesis, University of California Santa Barbara (NCEAS-UCSB)' % datetime.now().year
+author = 'Ian Nesbitt'
+
+# The short X.Y version
+sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+from pdgpoints._version import __version__ as version
+# The full version, including alpha/beta/rc tags
+release = version
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.autosectionlabel',
+    'sphinx.ext.githubpages',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'en'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+#pygments_style = None
+pygments_style = 'sphinx'
+
+
+# autosummary
+#autosummary_generate = True
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+html_logo = '_static/logo.png'
+
+#html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'vizpointsdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'vizpoints.tex', project+' Documentation',
+     author, 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, project, project+' Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, project, project+' Documentation',
+     author, project, 'Convert lidar data (LAZ, LAS, etc.) to 3dtiles',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    'python 3': ('https://docs.python.org/3', None),
+    'pyproj [stable]': ('https://pyproj4.github.io/pyproj/stable', None),
+    'pyegt [stable]': ('https://iannesbitt.github.io/pyegt', None),
+    }
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True