{"id":20282223,"url":"https://github.com/ubccr/harrier","last_synced_at":"2025-07-07T04:08:37.725Z","repository":{"id":17342784,"uuid":"20114136","full_name":"ubccr/harrier","owner":"ubccr","description":"screen to beam image targeting","archived":false,"fork":false,"pushed_at":"2023-05-01T20:56:49.000Z","size":1021,"stargazers_count":1,"open_issues_count":2,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-03-04T03:28:05.177Z","etag":null,"topics":["diffraction-analysis","image-analysis","x-ray-crystallography"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ubccr.png","metadata":{"files":{"readme":"README.rst","changelog":"ChangeLog","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.rst","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2014-05-23T21:10:27.000Z","updated_at":"2021-12-09T03:17:31.000Z","dependencies_parsed_at":"2025-01-14T07:41:22.932Z","dependency_job_id":"dd3e1eca-8e89-46b6-b011-d5ff501eeaa4","html_url":"https://github.com/ubccr/harrier","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ubccr/harrier","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ubccr%2Fharrier","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ubccr%2Fharrier/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ubccr%2Fharrier/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ubccr%2Fharrier/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ubccr","download_url":"https://codeload.github.com/ubccr/harrier/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ubccr%2Fharrier/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264010949,"owners_count":23543716,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["diffraction-analysis","image-analysis","x-ray-crystallography"],"created_at":"2024-11-14T14:08:35.908Z","updated_at":"2025-07-07T04:08:37.709Z","avatar_url":"https://github.com/ubccr.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"===============================================================================\nHarrier - screen to beam image targeting\n===============================================================================\n\n.. image:: docs/harrier-logo.jpg\n\n------------------------------------------------------------------------\nWhat is Harrier?\n------------------------------------------------------------------------\n\nIn the field of X-ray crystallography, images obtained from crystallization\nexperiments need to be interpreted for successful outcomes (crystals). If\nsuccess occurs, images of mounted crystals are later used to position them\nappropriate to the X-ray beam for diffraction analysis.  \n\nHarrier is a web application optimized for touch screen devices that provides a\nhaptic interface to the visualization, classification, and notation of\nexperimental crystallization data. Images from crystallization outcomes are\npresented allowing the user to select features of the image. The positions are\ncaptured by Harrier and converted to coordinates of the screening plate. The\nset of features can be exported using a REST based endpoint and used by a\nmounting robot for X-ray evaluation of the initial screening result.\n\nHarrier links the analysis of crystallization outcomes to the subsequent\ndiffraction analysis eliminating an initial optimization step and enabling\ncrystallization screening plates to be analyzed in the beam efficiently.\n\nLive demo `here \u003chttp://harrier.ccr.buffalo.edu\u003e`_.\n\n------------------------------------------------------------------------\nInstall\n------------------------------------------------------------------------\n\nInstalling from source::\n    \n    $ git clone git://github.com/ubccr/harrier.git harrier\n    $ cd harrier\n    $ pip install -r requirements.txt\n    $ python setup.py install\n\nRun Harrier in Docker container::\n\n    $ docker build -t harrier .\n    $ docker run -it --rm --name harrier \\\n         -p 5000:5000 harrier runserver --host=0.0.0.0\n\n------------------------------------------------------------------------\nQuick Start\n------------------------------------------------------------------------\n\n*Note* Any targets you create will be stored in memory only. To store targets\nin a database see next section. \n\n1. Run the harrier web server::\n\n    $ harrier runserver\n    [INFO]  * Running on http://127.0.0.1:5000/\n\n2. Open your web browser to http://127.0.0.1:5000/\n    \n3. Import image set library. Upload an image set library in CSV format.\n\n4. Add Targets. Use the interface to click on image features. The coordinates\n   of each target will be saved.\n\n5. Share. Export the image feature targets and share with external services,\n   for example an X-ray beam etc.\n\n------------------------------------------------------------------------\nSave results to sqlite database\n------------------------------------------------------------------------\n\n1. First create database directory and configuration file::\n\n    $ mkdir target-data\n    $ cd target-data\n    $ vim harrier.cfg\n    import os\n    _basedir = os.path.abspath(os.path.dirname(__file__))\n    SQLALCHEMY_DATABASE_URI = 'sqlite:///' + os.path.join(_basedir, 'harrier.db')\n\n2. Create empty databse, run the server::\n\n    $ harrier -c /path/to/target-data/harrier.cfg db rebuild\n    $ harrier -c /path/to/target-data/harrier.cfg runserver\n    [INFO]  * Running on http://127.0.0.1:5000/\n    \n3. Open your web browser to http://127.0.0.1:5000/ and load image set. Any targets\n   you add will be saved to the harrier.db sqlite database and persist after\n   Harrier is shutdown.\n\n------------------------------------------------------------------------\nImage Set CSV Format\n------------------------------------------------------------------------\n\nImage set libraries can be imported in a simple CSV format. The fields are as\nfollows::\n\n    [image name],[image url],[category]\n\nThe last field (category) is optional. For example, lysozyme images from plate\nX000014542 are stored in a file called X000014542-images.csv::\n\n    1488,http://localhost/drops/X000014542/X0000145421488201407081119.jpg\n    1175,http://localhost/drops/X000014542/X0000145421175201407081123.jpg\n    61,http://localhost/drops/X000014542/X0000145420061201407081137.jpg\n\nSee the data/ directory from the harrier source distribution. To import from\nthe command line run::\n\n    $ harrier -c /path/to/target-data/harrier.cfg load -f X000014542-images.csv\n\n------------------------------------------------------------------------\nRun using uWSGI\n------------------------------------------------------------------------\n\nTo run Harrier using uWSGI::\n\n    $ pip install uwsgi\n    $ cd [path to harrier]\n    $ uwsgi --socket 127.0.0.1:5000 --protocol=http -w wsgi:application\n\n------------------------------------------------------------------------\nLicense\n------------------------------------------------------------------------\n\nHarrier is released under the GNU General Public License (\"GPL\") Version 3.0.\nSee the LICENSE file.\n\n------------------------------------------------------------------------\nScreenshot\n------------------------------------------------------------------------\n\n.. image:: docs/harrier-screen-shot.png\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fubccr%2Fharrier","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fubccr%2Fharrier","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fubccr%2Fharrier/lists"}