Merge pull request #23 from Topp-Roots-Lab/development

Improve documentation and add basic tests for scaling

Author: tparkerd

CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/tparkerd/rawtools/issues.
+Report bugs at https://github.com/Topp-Roots-Lab/python-rawtools/issues.
 
 If you are reporting a bug, please include:
 
@@ -45,7 +45,7 @@ articles, and such.
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/tparkerd/rawtools/issues.
+The best way to send feedback is to file an issue at https://github.com/Topp-Roots-Lab/python-rawtools/issues.
 
 If you are proposing a feature:
 
@@ -103,7 +103,7 @@ Before you submit a pull request, check that it meets these guidelines:
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
 3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
-   https://travis-ci.com/tparkerd/rawtools/pull_requests
+   https://travis-ci.com/Topp-Roots-Lab/python-rawtools/pull_requests
    and make sure that the tests pass for all supported Python versions.
 
 Tips

HISTORY.rst

@@ -2,6 +2,23 @@
 History
 =======
 
+0.3.0 (2021-07-18)
+------------------
+
+Added
+*****
+
+* License
+* Basic tests on core functionality for scaling data
+
+Changed
+*******
+
+* Updated URL for any references to GitHub repo
+* Updated docstring header for `raw2img` module
+* Updated README to be more descriptive
+
+
 0.2.0 (2021-01-04)
 ------------------
 

LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2021, Topp Lab, Donald Danforth Plant Science Center
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.rst

@@ -1,25 +1,38 @@
-=========
+
 RAW Tools
 =========
 
+Utility library for consuming and manipulating x-ray volume data in ``.raw`` format.
 
+Features
+--------
 
 
+* Convert float32, uint16, and uint8 versions of ``.raw`` XRT volume data
+* Extract image slices from ``.raw`` files
+* Read, parse, and generate metadata files (\ ``.dat``\ ) for XRT data
+* Convert proprietary ``.nsihdr`` files into ``.raw`` format (Windows only). Batch conversion supported as CLI and minimal GUI.
+* Generate previews of XRT volumes for quality control (e.g., maximum density projections, midslice extraction, etc.)
 
+Planned Features
+----------------
 
-Utility library for consuming and manipulating x-ray data in RAW format
 
+* Generate dummy ``.raw`` files for testing downstream pipelines
+* Batch conversion of ``.nsihdr`` on Linux systems
+* Density adjustment (similar to automated adjustment MATLAB scripts for ``rootseg``\ )
 
+Related Projects
+----------------
 
-Features
---------
 
-* TODO
+* `xrcap <https://github.com/Topp-Roots-Lab/3d-root-crown-analysis-pipeline>`_\ : root crown image analysis pipeline
+* `DyanmicRoots <https://github.com/Topp-Roots-Lab/DynamicRoots>`_\ : tool for reconstructing and analyzing the growth of a plant root system
+* TopoRoot (\ *tentative name*\ )
+* `rootseg <https://github.com/Topp-Roots-Lab/rootseg>`_\ : ML-based segmentation for soil rich samples
+* `xrt-dmt <https://github.com/Topp-Roots-Lab/xrt-dmt>`_\ : data management tool for tracking and archiving XRT (meta)data
 
 Credits
 -------
 
-This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
-
-.. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
+This package was created with `Cookiecutter <https://github.com/audreyr/cookiecutter-pypackage>`_ and the `audreyr/cookiecutter-pypackage <https://github.com/audreyr/cookiecutter-pypackage>`_ project template.