Commit 26f80bd4 authored by aknecht2's avatar aknecht2

Documentation update -- added publications.

parent c5c28ee8
......@@ -51,17 +51,9 @@ This script shows how to get started with ih. Let's talk about it block by bloc
import ih.imgproc
plant = ih.imgproc.Image("/path/to/your/image")
These two lines setup your image. The first line imports a module, which is simply
a grouping of related in code. In this case, we import the 'imgproc' module, which
is a grouping of functions related to image processing. This module contains
all of ih's image processing functionality, and as a result, is the code we want to import
to process images. The second line creates an Image object named 'plant'.
Object Oriented Programming (OOP) can be a hard concept to understand at first.
In a simplistic form, objects are like nouns, and the methods we perform on the objects
are like verbs. Our Image object has certain properties that make it that type of object,
just like plants have properties that define them. This line accomplishes translating
the actual image into a form understandable by the code. The 'plant' object now has
properties that define it, and actions (methods) we can perform on it. The rest of the script
These two lines setup your image. The first line imports the ih imgproc module, this module contains
all of ih's image processing functionality. The second line creates an Image object named 'plant'.
The plant object now has properties that define it, and methods we can perform on it. The rest of the script
deals specifically with the methods we can perform on our image objects.
.. code-block:: python
......
Welcome to Image Harvest documentation!
==============================================================
Link to GitHub: `ih <https://git.unl.edu/aknecht2/ih/>`_
`GitHub <https://git.unl.edu/aknecht2/ih/>`_
`Sample Images <http://cropstressgenomics.org/data/subset.tar.gz>`_
To obtain access to a larger set of rice images (RGB, FLUO, NIR, IR), please contact PI: H. Walia
* Publications:
* Campbell MT, Knecht AC, Berger B, Brien CJ, Wang D, Walia H. Integrating Image-Based Phenomics and Association Analysis to Dissect the Genetic Architecture of Temporal Salinity Responses in Rice. 2015, Plant Physiology. `Link <http://www.plantphysiol.org/content/early/2015/06/25/pp.15.00450.short>`_.
* Knecht AC, Campbell MT, Caprez A, Swanson DR, Walia H. Image Harvest: An open source platform for high-throughput plant image processing and analysis. 2016, JXB. (In press).
* `Developing a processing workflow on a local computer <http://cropstressgenomics.org/data/html/ex_script_camera2.html>`_
* `Executing processing workflows on a computing cluster <http://cropstressgenomics.org/data/html/ex_workflow_1.html>`_
Contents:
......
......@@ -216,7 +216,3 @@ list as above that is, `numpy <http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy>
One final note, when loading images, python expects forward slashes not back slashes,
and does not expect the C: for absolute paths. If you have an image called "test.jpg"
in your downloads folder, the correct path for python is "/Users/username/Downloads/test.jpg".
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