Initial commit

Flexbrdf/docs/source/.#about.rst

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+adam@adams-mbp.russell.wisc.edu.34021

Flexbrdf/docs/source/_static/css/main.scss

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+---
+# Only the main Sass file needs front matter (the dashes are enough)
+---
+
+@import "minimal-mistakes/skins/{{ site.minimal_mistakes_skin | default: 'default' }}"; // skin
+@import "minimal-mistakes"; // main partials
+
+html {
+  font-size: 16px; // change to whatever
+}

Flexbrdf/docs/source/_static/css/slider.css

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+.beer-slider{display:inline-block;overflow:hidden;position:relative}.beer-slider *,.beer-slider:after,.beer-slider :after,.beer-slider:before,.beer-slider :before{box-sizing:border-box}.beer-slider img,.beer-slider svg{vertical-align:bottom}.beer-slider>*{height:100%}.beer-slider>img{height:auto;max-width:100%}.beer-reveal{left:0;opacity:0;overflow:hidden;position:absolute;right:50%;top:0;transition:opacity .35s;z-index:1}.beer-reveal>:first-child{height:100%;max-width:none;width:200%}.beer-reveal>img:first-child{height:auto}.beer-range{-moz-appearance:none;-ms-touch-action:auto;-webkit-appearance:slider-horizontal!important;bottom:0;cursor:pointer;height:100%;left:-1px;margin:0;opacity:0;position:absolute;top:0;touch-action:auto;width:calc(100% + 2px);z-index:2}.beer-range::-webkit-slider-thumb{-webkit-appearance:none;height:300vh}.beer-range::-moz-range-thumb{-webkit-appearance:none;height:300vh}.beer-range::-ms-tooltip{display:none}.beer-handle{background:hsla(0,0%,100%,.5);border-radius:50%;box-shadow:0 0 6px transparent;color:#000;height:48px;left:50%;opacity:0;pointer-events:none;position:absolute;top:50%;transform:translate3d(-50%,-50%,0);transition:background .3s,box-shadow .3s,opacity .5s .25s;width:48px;z-index:2}.beer-handle:after,.beer-handle:before{border-left:2px solid;border-top:2px solid;content:"";height:10px;position:absolute;top:50%;transform-origin:0 0;width:10px}.beer-handle:before{left:10px;transform:rotate(-45deg)}.beer-handle:after{right:0;transform:rotate(135deg)}.beer-range:focus~.beer-handle{background:hsla(0,0%,100%,.85);box-shadow:0 0 3px rgba(0,0,0,.4)}.beer-reveal[data-beer-label]:after,.beer-slider[data-beer-label]:after{background:hsla(0,0%,100%,.75);border-radius:.125rem;content:attr(data-beer-label);line-height:1;padding:.5rem;position:absolute;top:1.5rem}.beer-slider[data-beer-label]:after{right:1.5rem}.beer-reveal[data-beer-label]:after{left:1.5rem}.beer-reveal[data-beer-label=""]:after,.beer-slider[data-beer-label=""]:after{content:none}.beer-ready .beer-handle,.beer-ready .beer-reveal{opacity:1}

Flexbrdf/docs/source/algorithms.rst

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+.. _algorithms:
+
+
+==================
+ Advanced use 
+==================
+
+Spectrum resampling
+===================
+
+.. todo:: Spectrum resampling example script
+
+Topographic correction
+======================
+
+.. todo:: Topographic correction example script
+
+BRDF correction
+===============
+
+.. todo:: BRDF correction example script
+

Flexbrdf/docs/source/basics.rst

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+.. _basics:
+
+===========
+ Basic use
+===========
+
+
+Loading images
+==============
+
+HyTools includes options for loading both ENVI formatted binary files, NASA NetCDF files,
+and NEON AOP HDF files.
+
+.. code-block:: python
+
+   import hytools as ht
+
+   #Create a HyTools container object 
+   envi = ht.HyTools()
+
+   #Read and load file metadata
+   envi.read_data('./envi_file.bin',file_type= 'envi')
+
+For reading NEON data the process is the same:
+
+.. code-block:: python
+		
+   #Load an NEON HDF image
+   neon = ht.HyTools()
+   neon.read_data("./neon_file.h5",'neon')
+     
+  
+Reading data
+============
+
+There are several ways to read data using a :class:`~hytools.base.HyTools` object. One option
+is to use one of the 'get' methods:
+
+.. code-block:: python
+
+	wave = neon.get_wave(900)		
+	band = neon.get_band(10)
+	column = neon.get_column(1)
+	line = neon.get_line(234)
+	chunk = neon.get_chunk(x1,x2,y1,y2)
+	pixels = neon.get_pixels([0,1,2],[3,4,5])
+	
+We can also retrieve masked data, where a binary mask is used to
+return a subset of the data. Currently masking only works using the
+:meth:`~hytools.base.HyTools.get_band` or
+:meth:`~hytools.base.HyTools.get_wave` methods. First we need to
+generate a mask, which can be done using the
+:meth:`~hytools.base.HyTools.gen_mask` method.
+
+.. code-block:: python
+
+	# NDVI masking function	
+	def masker(hy_obj):
+	    ir = hy_obj.get_wave(900)
+	    red = hy_obj.get_wave(660)
+	    ndvi = (ir-red)/(ir+red)
+	    return ndvi > .5	
+
+	# Generate mask
+	neon.gen_mask(masker)
+
+	# Retrieve pixels where mask is True
+	pixels = neon.get_band(100, mask_values = True)
+	
+
+Alternatively an :class:`~hytools.base.Iterator` can be used to cycle along a
+specified axis of the dataset either by line, column, band or
+chunk. This is useful for cycling through and image, applying
+a function/algorithm and then writing to a file.
+
+.. code-block:: python
+		
+   iterator = hy_obj.iterate(by = 'line')
+
+Next cycle through the image line by line until complete:
+
+.. code-block:: python
+		
+   while not iterator.complete:  
+       line = iterator.read_next() 
+
+
+Writing data
+============
+
+Currently writing is only supported for ENVI files and NetCDF files, however data from
+NEON hdf files can be easy written to ENVI format using builtin
+functions.
+
+First an ENVI header dictionary needs to be generated to specify the
+file size, datatype, interleave and other relevant metadata. This is
+done using the :func:`~hytools.io.envi.envi_header_from_hdf` function.
+
+.. code-block:: python
+
+    header_dict = envi_header_from_hdf(neon)
+
+In this case we are going to export an RGBI image so we need to update
+the number of bands:
+
+.. code-block:: python
+
+   head_dict['bands'] = 4
+    
+Next we create an :class:`~hytools.io.envi.WriteENVI` object which
+generates the header and image file using the specifications in the
+header dictionary:
+
+.. code-block:: python
+
+    output_name = './neon.bin'
+    writer = WriteENVI(output_name,header_dict)
+
+Finally we can write the bands to file. First we retrieve the closest
+wavelength to each input wavelength using the
+:meth:`~hytools.base.HyTools.get_wave` method, next we write the band
+to the new file with the :meth:`~hytools.io.envi.WriteENVI.write_band`
+method.
+
+.. code-block:: python
+
+   for band_num,wavelength enumerate([660,550,440,880]):
+       wave = neon.get_wave(wavelength)
+       writer.write_band(wave,band_num)
+   writer.close()
+		
+
+
+
+
+
+
+
+
+
+

Flexbrdf/docs/source/command_line.rst

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+.. _command:
+
+====================
+ Command line tools
+====================
+
+
+image_correct.py
+================
+
+The 'image_correct' script is a general purpose tool that utilizes
+topographic, BRDF and wavelength resampling fuctions to modify/correct
+an image.
+
+Configuration file
+------------------
+
+Image correction options are specified using a JSON file. Example
+configuration files can be found in the github repository. We
+have also created a script to automatically generates a JSON
+configuration file.
+
+
+
+trait_estimate.py
+=================
+
+The 'trait_estimate.py' script is a tool to generate maps of canopy
+foliar traits given a set of model parameters. Currently only PLSR
+models are supported, however support for other statistical modeling
+frameworks like Gaussian process regression is currently under
+development.
+
+
+

Flexbrdf/docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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.
+# sphinx-apidoc -f -o source/ ../hytools
+#
+import os
+import sys
+import sphinx_rtd_theme
+sys.path.insert(0, os.path.abspath('..'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'HyTools'
+copyright = '2020, Adam Chlus, Zhiwei Ye, Philip Townsend'
+author = 'Adam Chlus'
+
+# The full version, including alpha/beta/rc tags
+release = '0.0.1'
+
+html_static_path = ['_static']
+
+html_css_files = [
+    'css/slider.css',
+]
+
+html_js_files = [
+    'js/slider.js',
+]
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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.napoleon',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.coverage',
+    'sphinx_rtd_theme',
+    'sphinx.ext.todo'
+]
+
+todo_include_todos=True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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 = []
+
+master_doc = 'index'
+# -- 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'
+
+# 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']

Flexbrdf/docs/source/contents.rst

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+About HyTools
+=====================
+
+HyTools is a python library for processing airborne and spaceborne
+imaging spectroscopy data, with a focus on terrestrial scenes. At it's
+core it consists of functions for reading and writing `ENVI
+<https://www.l3harrisgeospatial.com/docs/ENVIImageFiles.html>`_
+formatted images and reading `NEON AOP
+<https://www.neonscience.org/data-collection/airborne-remote-sensing>`_
+HDF files along with a series of image processing functions including
+spectral resampling, topographic and BRDF correction, spectral
+transforms, masking and more. We have also created a series of command
+line tools which combine these functions and provide a streamlined
+workflow for processing images.
+
+Examples
+--------
+
+BRDF correction
+~~~~~~~~~~~~~~~
+
+.. raw:: html
+	 
+  <embed>
+
+  <link rel="stylesheet" href="/_static/css/slider.css">
+  <script src="/_static/js/slider.js" type="text/javascript" ></script>
+
+  <div id="slider" class="beer-slider" data-beer-label="">
+     <img src="/_static/images/research/3d_rgb.jpg" alt="">
+     <div class="beer-reveal" data-beer-label="">
+        <img src="/_static/images/research/rgb_rgb.jpg" alt="">
+     </div>
+   </div>
+
+   <script type="text/javascript">
+       new BeerSlider(document.getElementById('slider'));
+   </script>
+
+   </embed>
+
+  
+
+.. image:: brdf_before_after.png
+
+Topographic correction
+~~~~~~~~~~~~~~~~~~~~~~
+.. image:: topo_correct.gif	   
+
+	   

Flexbrdf/docs/source/hytools.correction.rst

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+hytools.correction package
+==========================
+
+Submodules
+----------
+
+hytools.correction.brdf module
+------------------------------
+
+.. automodule:: hytools.correction.brdf
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+hytools.correction.topo module
+------------------------------
+
+.. automodule:: hytools.correction.topo
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: hytools.correction
+   :members:
+   :undoc-members:
+   :show-inheritance:

Flexbrdf/docs/source/hytools.io.rst

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+hytools.io package
+==================
+
+Submodules
+----------
+
+hytools.io.envi module
+----------------------
+
+.. automodule:: hytools.io.envi
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+hytools.io.neon module
+----------------------
+
+.. automodule:: hytools.io.neon
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+hytools.io.netcdf module
+----------------------
+
+.. automodule:: hytools.io.netcdf
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: hytools.io
+   :members:
+   :undoc-members:
+   :show-inheritance:

Flexbrdf/docs/source/hytools.misc.rst

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+hytools.misc package
+====================
+
+Submodules
+----------
+
+hytools.misc.misc module
+------------------------
+
+.. automodule:: hytools.misc.misc
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: hytools.misc
+   :members:
+   :undoc-members:
+   :show-inheritance:

Flexbrdf/docs/source/hytools.rst

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+hytools package
+===============
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   hytools.correction
+   hytools.io
+   hytools.misc
+   hytools.transform
+
+Submodules
+----------
+
+hytools.base module
+-------------------
+
+.. automodule:: hytools.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: hytools
+   :members:
+   :undoc-members:
+   :show-inheritance:

Flexbrdf/docs/source/hytools.transform.rst

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+hytools.transform package
+=========================
+
+Submodules
+----------
+
+hytools.transform.mnf module
+----------------------------
+
+.. automodule:: hytools.transform.mnf
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+hytools.transform.resampling module
+-----------------------------------
+
+.. automodule:: hytools.transform.resampling
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: hytools.transform
+   :members:
+   :undoc-members:
+   :show-inheritance:

Flexbrdf/docs/source/index.rst

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+HyTools Documentation
+=====================
+
+.. toctree::
+   :maxdepth: 2
+
+   contents	      
+   installation
+   basics
+   algorithms
+   command_line
+   modules

Flexbrdf/docs/source/installation.rst

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+.. _install:
+
+=============
+ Installation
+=============
+
+
+Dependencies
+============
+
+   * numpy
+   * h5py
+   * ray
+     
+Installing HyTools
+==================
+To download to hytools simply clone the github repository
+
+.. code-block:: shell
+     
+   $ git clone https://github.com/EnSpec/hytools.git
+ 
+
+and run the following command inside the hytools folder to install
+
+.. code-block:: shell
+     
+   $ python setup.py install
+

Flexbrdf/docs/source/modules.rst

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+hytools
+=======
+
+.. toctree::
+   :maxdepth: 4
+
+   hytools

Flexbrdf/docs/source/requirements.txt

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+sphinx_rtd_theme