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https://github.com/ubccr/harrier

screen to beam image targeting
https://github.com/ubccr/harrier

diffraction-analysis image-analysis x-ray-crystallography

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screen to beam image targeting

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README 

        
===============================================================================

Harrier - screen to beam image targeting

===============================================================================



.. image:: docs/harrier-logo.jpg



------------------------------------------------------------------------

What is Harrier?

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In the field of X-ray crystallography, images obtained from crystallization

experiments need to be interpreted for successful outcomes (crystals). If

success occurs, images of mounted crystals are later used to position them

appropriate to the X-ray beam for diffraction analysis.  



Harrier is a web application optimized for touch screen devices that provides a

haptic interface to the visualization, classification, and notation of

experimental crystallization data. Images from crystallization outcomes are

presented allowing the user to select features of the image. The positions are

captured by Harrier and converted to coordinates of the screening plate. The

set of features can be exported using a REST based endpoint and used by a

mounting robot for X-ray evaluation of the initial screening result.



Harrier links the analysis of crystallization outcomes to the subsequent

diffraction analysis eliminating an initial optimization step and enabling

crystallization screening plates to be analyzed in the beam efficiently.



Live demo `here `_.



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Install

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Installing from source::

    

    $ git clone git://github.com/ubccr/harrier.git harrier

    $ cd harrier

    $ pip install -r requirements.txt

    $ python setup.py install



Run Harrier in Docker container::



    $ docker build -t harrier .

    $ docker run -it --rm --name harrier \

         -p 5000:5000 harrier runserver --host=0.0.0.0



------------------------------------------------------------------------

Quick Start

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*Note* Any targets you create will be stored in memory only. To store targets

in a database see next section. 



1. Run the harrier web server::



    $ harrier runserver

    [INFO]  * Running on http://127.0.0.1:5000/



2. Open your web browser to http://127.0.0.1:5000/

    

3. Import image set library. Upload an image set library in CSV format.



4. Add Targets. Use the interface to click on image features. The coordinates

   of each target will be saved.



5. Share. Export the image feature targets and share with external services,

   for example an X-ray beam etc.



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Save results to sqlite database

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1. First create database directory and configuration file::



    $ mkdir target-data

    $ cd target-data

    $ vim harrier.cfg

    import os

    _basedir = os.path.abspath(os.path.dirname(__file__))

    SQLALCHEMY_DATABASE_URI = 'sqlite:///' + os.path.join(_basedir, 'harrier.db')



2. Create empty databse, run the server::



    $ harrier -c /path/to/target-data/harrier.cfg db rebuild

    $ harrier -c /path/to/target-data/harrier.cfg runserver

    [INFO]  * Running on http://127.0.0.1:5000/

    

3. Open your web browser to http://127.0.0.1:5000/ and load image set. Any targets

   you add will be saved to the harrier.db sqlite database and persist after

   Harrier is shutdown.



------------------------------------------------------------------------

Image Set CSV Format

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Image set libraries can be imported in a simple CSV format. The fields are as

follows::



    [image name],[image url],[category]



The last field (category) is optional. For example, lysozyme images from plate

X000014542 are stored in a file called X000014542-images.csv::



    1488,http://localhost/drops/X000014542/X0000145421488201407081119.jpg

    1175,http://localhost/drops/X000014542/X0000145421175201407081123.jpg

    61,http://localhost/drops/X000014542/X0000145420061201407081137.jpg



See the data/ directory from the harrier source distribution. To import from

the command line run::



    $ harrier -c /path/to/target-data/harrier.cfg load -f X000014542-images.csv



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Run using uWSGI

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To run Harrier using uWSGI::



    $ pip install uwsgi

    $ cd [path to harrier]

    $ uwsgi --socket 127.0.0.1:5000 --protocol=http -w wsgi:application



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License

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Harrier is released under the GNU General Public License ("GPL") Version 3.0.

See the LICENSE file.



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Screenshot

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.. image:: docs/harrier-screen-shot.png