Metadata-Version: 2.1
Name: ibeis
Version: 2.2.3
Summary: Image Based Ecological Information System
Home-page: UNKNOWN
Author: Jon Crall, Jason Parham
Author-email: erotemic@gmail.com
License: UNKNOWN
Description: |ReadTheDocs| |Pypi| |Downloads| |Codecov| |CircleCI| |Travis| |Appveyor| 
        
        .. image:: https://i.imgur.com/L0k84xQ.png
        
        This project is a component of the WildMe / WildBook project: See https://github.com/WildbookOrg/
        
        
        IBEIS - Image Analysis 
        ----------------------
        
        I.B.E.I.S. = Image Based Ecological Information System
        ------------------------------------------------------
        
        .. image:: http://i.imgur.com/TNCiEBe.png
            :alt: "(Note: the rhino and wildebeest mathces may be dubious. Other species do work well though")
        
        Program Description
        -------------------
        
        IBEIS program for the storage and management of images and derived data for
        use in computer vision algorithms. It aims to compute who an animal is, what
        species an animal is, and where an animal is with the ultimate goal being to
        ask important why biological questions.  This This repo Image Analysis image
        analysis module of IBEIS. It is both a python module and standalone program. 
        
        Currently the system is build around and SQLite database, a PyQt4 GUI, and
        matplotlib visualizations. Algorithms employed are: random forest species
        detection and localization, hessian-affine keypoint detection, SIFT keypoint
        description, LNBNN identification using approximate nearest neighbors.
        Algorithms in development are SMK (selective match kernel) for identification
        and deep neural networks for detection and localization. 
        
        The core of IBEIS is the IBEISController class. It provides an API into IBEIS
        data management and algorithms. The IBEIS API Documentation can be found here:
        `http://erotemic.github.io/ibeis`
        
        The IBEIS GUI (graphical user interface) is built on top of the API. 
        We are also experimenting with a new web frontend that bypasses the older GUI code.
        
        ## Self Installing Executables:
        
        Unfortunately we have not released self-installing-executables for IBEIS yet. 
        We plan to release these "soon". 
        
        However there are old HotSpotter (the software which IBEIS is based on)
        binaries available. These can be downloaded from: `http://cs.rpi.edu/hotspotter/`
        
        Visual Demo
        -----------
        
        
        .. image:: http://i.imgur.com/QWrzf9O.png
           :width: 600
           :alt: Feature Extraction
        
        .. image:: http://i.imgur.com/iMHKEDZ.png
           :width: 600
           :alt: Nearest Neighbors
        
        
        Match Scoring 
        -------------
        
        .. image:: http://imgur.com/Hj43Xxy.png
           :width: 600
           :alt: Match Inspection
        
        Spatial Verification
        --------------------
        
        .. image:: http://i.imgur.com/VCz0j9C.jpg
           :width: 600
           :alt: sver
        
        
        .. code:: bash
        
            python -m vtool.spatial_verification --test-spatially_verify_kpts --show
        
        Name Scoring
        ------------
        
        .. image:: http://i.imgur.com/IDUnxu2.jpg
           :width: 600
           :alt: namematch
        
        
        .. code:: bash
        
            python -m ibeis.algo.hots.chip_match show_single_namematch --qaid 1 --show
        
        Identification Ranking 
        ----------------------
        
        .. image:: http://i.imgur.com/BlajchI.jpg
           :width: 600
           :alt: rankedmatches
        
        
        .. code:: bash
        
            python -m ibeis.algo.hots.chip_match show_ranked_matches --show --qaid 86
        
        Inference
        ---------
        
        .. image:: http://i.imgur.com/RYeeENl.jpg
           :width: 600
           :alt: encgraph
        
        
        .. code:: bash
        
            # broken
            # python -m ibeis.algo.preproc.preproc_encounter compute_encounter_groups --show
        
        Internal Modules
        ----------------
        
        In the interest of modular code we are actively developing several different modules. 
        
        
        Erotemic's IBEIS Image Analysis module dependencies 
        
        * https://github.com/Erotemic/utool
        
        * https://github.com/Erotemic/plottool_ibeis
        * https://github.com/Erotemic/vtool_ibeis
        * https://github.com/Erotemic/guitool_ibeis
        * https://github.com/Erotemic/pyflann_ibeis
        
        * https://github.com/Erotemic/hesaff
        * https://github.com/Erotemic/futures_actors
        
        
        bluemellophone's IBEIS Image Analysis modules
        
        * https://github.com/WildbookOrg/detecttools
        * https://github.com/WildbookOrg/pyrf
          docs: http://bluemellophone.github.io/pyrf
        
        
        The IBEIS module itself: 
        
        * https://github.com/WildbookOrg/ibeis
        
        IBEIS Development Environment Setup 
        ------------------------------------
        
        NOTE: this section is outdated.
        
        .. code:: bash
        
            # The following install script install ibeis and all dependencies. 
            # If it doesnt you can look at the older instructions which follow
            # and try to figure it out. After running this you should have a code
            # directory with all of the above repos. 
        
            # Navigate to your code directory
            export CODE_DIR=~/code
            mkdir $CODE_DIR
            cd $CODE_DIR
        
            # Clone IBEIS
            git clone https://github.com/Erotemic/ibeis.git
            cd ibeis
        
            # Install the requirements for super_setup
            pip install -r requirements/super_setup.txt
        
            # Install the development requirements (note-these are now all on pypi, so
            # this is not strictly necessary)
            python super_setup.py ensure
        
            # NOTE: you can use super_setup to do several things
            python super_setup.py --help
            python super_setup.py versions
            python super_setup.py status
            python super_setup.py check
            python super_setup.py pull
        
            # Run the run_developer_setup.sh file in each development repo
            python super_setup.py develop
        
            # Or you can also just do to use pypi versions of dev repos:
            python setup.py develop
        
            # Optional: set a workdir and download a test dataset
            .python -m ibeis.dev 
            .python -m ibeis.dev -t mtest 
            python -m ibeis.dev -t nauts 
            ./reset_dbs.py
        
            python -m ibeis --set-workdir ~/data/work --preload-exit
            python -m ibeis -e ensure_mtest
        
            # make sure everyhing is set up correctly
            python -m ibeis --db PZ_MTEST
        
        
        Running Tests
        -------------
        
        The new way of running tests is with xdoctest, or using the "run_doctests.sh" script.
        
        
        Example usage
        --------------
        
        (Note: This list is far from complete)
        
        .. code:: bash
        
            #--------------------
            # Main Commands
            #--------------------
            python -m ibeis.main <optional-arguments> [--help]
            python -m ibeis.dev <optional-arguments> [--help]
            # main is the standard entry point to the program
            # dev is a more advanced developer entry point
        
            # ** NEW 7-23-2015 **: the following commands are now equivalent and do not
            # have to be specified from the ibeis source dir if ibeis is installed
            python -m ibeis <optional-arguments> [--help]
            python -m ibeis.dev <optional-arguments> [--help]
        
            # Useful flags.
            # Read code comments in dev.py for more info.
            # Careful some commands don't work. Most do.
            # --cmd          # shows ipython prompt with useful variables populated
            # -w, --wait     # waits (useful for showing plots)
            # --gui          # starts the gui as well (dev.py does not show gui by default, main does)
            # --web          # runs the program as a web server
            # --quiet        # turns off most prints
            # --verbose      # turns on verbosity
            # --very-verbose # turns on extra verbosity
            # --debug2       # runs extra checks
            # --debug-print  # shows where print statments occur
            # -t [test]
        
        
            #--------------------
            # PSA: Workdirs:
            #--------------------
            # IBEIS uses the idea of a work directory for databases.
            # Use --set-workdir <path> to set your own, or a gui will popup and ask you about it
            ./main.py --set-workdir /raid/work --preload-exit
            ./main.py --set-logdir /raid/logs/ibeis --preload-exit
        
            python -m ibeis.dev --set-workdir ~/data/work --preload-exit
        
            # use --db to specify a database in your WorkDir
            # --setdb makes that directory your default directory
            python -m ibeis.dev --db <dbname> --setdb
        
            # Or just use the absolute path
            python -m ibeis.dev --dbdir <full-dbpath>
        
        
            #--------------------
            # Examples:
            # Here are are some example commands
            #--------------------
            # Run the queries for each roi with groundtruth in the PZ_MTEST database
            # using the best known configuration of parameters
            python -m ibeis.dev --db PZ_MTEST --allgt -t best
            python -m ibeis.dev --db PZ_MTEST --allgt -t score
        
        
            # View work dir
            python -m ibeis.dev --vwd --prequit
        
            # List known databases
            python -m ibeis.dev -t list_dbs
        
        
            # Dump/Print contents of params.args as a dict
            python -m ibeis.dev --prequit --dump-argv
        
            # Dump Current SQL Schema to stdout 
            python -m ibeis.dev --dump-schema --postquit
        
        
            #------------------
            # Convert a hotspotter database to IBEIS
            #------------------
        
            # NEW: You can simply open a hotspotter database and it will be converted to IBEIS
            python -m ibeis convert_hsdb_to_ibeis --dbdir <path_to_hsdb>
        
            # This script will exlicitly conver the hsdb
            python -m ibeis convert_hsdb_to_ibeis --hsdir <path_to_hsdb> --dbdir <path_to_newdb>
        
            #---------
            # Ingest examples
            #---------
            # Ingest raw images
            python -m ibeis.dbio.ingest_database --db JAG_Kieryn
        
            #---------
            # Run Tests
            #---------
            ./run_tests.py
        
            #----------------
            # Test Commands
            #----------------
            # Set a default DB First
            python -m ibeis.dev --setdb --dbdir /path/to/your/DBDIR
            python -m ibeis.dev --setdb --db YOURDB
            python -m ibeis.dev --setdb --db PZ_MTEST
            python -m ibeis.dev --setdb --db PZ_FlankHack
        
            # List all available tests
            python -m ibeis.dev -t help
            # Minimal Database Statistics
            python -m ibeis.dev --allgt -t info
            # Richer Database statistics
            python -m ibeis.dev --allgt -t dbinfo
            # Print algorithm configurations
            python -m ibeis.dev -t printcfg
            # Print database tables
            python -m ibeis.dev -t tables
            # Print only the image table
            python -m ibeis.dev -t imgtbl
            # View data directory in explorer/finder/nautilus
            python -m ibeis.dev -t vdd
        
            # List all IBEIS databases
            python -m ibeis list_dbs
            # Delete cache
            python -m ibeis delete_cache --db testdb1
        
        
            # Show a single annotations
            python -m ibeis.viz.viz_chip show_chip --db PZ_MTEST --aid 1 --show
            # Show annotations 1, 3, 5, and 11
            python -m ibeis.viz.viz_chip show_many_chips --db PZ_MTEST --aids=1,3,5,11 --show
        
        
            # Database Stats for all our important datasets:
            python -m ibeis.dev --allgt -t dbinfo --db PZ_MTEST | grep -F "[dbinfo]"
        
            # Some mass editing of metadata
            python -m ibeis.dev --db PZ_FlankHack --edit-notes
            python -m ibeis.dev --db GZ_Siva --edit-notes
            python -m ibeis.dev --db GIR_Tanya --edit-notes
            python -m ibeis.dev --allgt -t dbinfo --db GZ_ALL --set-all-species zebra_grevys
        
            # Current Experiments:
        
            # Main experiments
            python -m ibeis --tf draw_annot_scoresep --db PZ_MTEST -a default -t best --show
            python -m ibeis.dev -e draw_rank_cdf --db PZ_MTEST --show -a timectrl
            # Show disagreement cases
            ibeis --tf draw_match_cases --db PZ_MTEST -a default:size=20 \
                -t default:K=[1,4] \
                --filt :disagree=True,index=0:4 --show
        
            # SMK TESTS
            python -m ibeis.dev -t smk2 --allgt --db PZ_MTEST --nocache-big --nocache-query --qindex 0:20
            python -m ibeis.dev -t smk2 --allgt --db PZ_MTEST --qindex 20:30 --va
        
            # Feature Tuning
            python -m ibeis.dev -t test_feats -w --show --db PZ_MTEST --allgt --qindex 1:2
        
            python -m ibeis.dev -t featparams -w --show --db PZ_MTEST --allgt
            python -m ibeis.dev -t featparams_big -w --show --db PZ_MTEST --allgt
        
            # NEW DATABASE TEST
            python -m ibeis.dev -t best --db seals2 --allgt
        
            # Testing Distinctivness Parameters
            python -m ibeis.algo.hots.distinctiveness_normalizer --test-get_distinctiveness --show --db GZ_ALL --aid 2
            python -m ibeis.algo.hots.distinctiveness_normalizer --test-get_distinctiveness --show --db PZ_MTEST --aid 10
            python -m ibeis.algo.hots.distinctiveness_normalizer --test-test_single_annot_distinctiveness_params --show --db GZ_ALL --aid 2
        
            # 2D Gaussian Curves
            python -m vtool_ibeis.patch --test-test_show_gaussian_patches2 --show
        
            # Test Keypoint Coverage
            python -m vtool_ibeis.coverage_kpts --test-gridsearch_kpts_coverage_mask --show
            python -m vtool_ibeis.coverage_kpts --test-make_kpts_coverage_mask --show
        
            # Test Grid Coverage
            python -m vtool_ibeis.coverage_grid --test-gridsearch_coverage_grid_mask --show
            python -m vtool_ibeis.coverage_grid --test-sparse_grid_coverage --show
            python -m vtool_ibeis.coverage_grid --test-gridsearch_coverage_grid --show
        
            # Test Spatially Constrained Scoring
            python -m ibeis.algo.hots.vsone_pipeline --test-compute_query_constrained_matches --show
            python -m ibeis.algo.hots.vsone_pipeline --test-gridsearch_constrained_matches --show
        
            # Test VsMany ReRanking
            python -m ibeis.algo.hots.vsone_pipeline --test-vsone_reranking --show
            python -m ibeis.algo.hots.vsone_pipeline --test-vsone_reranking --show --homog
        
            # Problem cases with the back spot
            python -m ibeis.algo.hots.vsone_pipeline --test-vsone_reranking --show --homog --db GZ_ALL --qaid 425
            python -m ibeis.algo.hots.vsone_pipeline --test-vsone_reranking --show --homog --db GZ_ALL --qaid 662
            python -m ibeis.dev -t custom:score_method=csum,prescore_method=csum --db GZ_ALL --show --va -w --qaid 425 --noqcache
            # Shows vsone results with some of the competing cases
            python -m ibeis.algo.hots.vsone_pipeline --test-vsone_reranking --show --homog --db GZ_ALL --qaid 662 --daid_list=425,342,678,233
        
            # More rerank vsone tests
            python -c "import utool as ut; ut.write_modscript_alias('Tbig.sh', 'dev.py', '--allgt  --db PZ_Master0')"
            sh Tbig.sh -t custom:rrvsone_on=True custom 
            sh Tbig.sh -t custom:rrvsone_on=True custom --noqcache
        
            #----
            # Turning back on name scoring and feature scoring and restricting to rerank a subset
            # This gives results that are closer to what we should actually expect
            python -m ibeis.dev --allgt -t custom \
                custom:rrvsone_on=True,prior_coeff=1.0,unconstrained_coeff=0.0,fs_lnbnn_min=0,fs_lnbnn_max=1 \
                custom:rrvsone_on=True,prior_coeff=0.5,unconstrained_coeff=0.5,fs_lnbnn_min=0,fs_lnbnn_max=1 \
                custom:rrvsone_on=True,prior_coeff=0.1,unconstrained_coeff=0.9,fs_lnbnn_min=0,fs_lnbnn_max=1 \
                --print-bestcfg
            #----
        
            #----
            # VsOneRerank Tuning: Tune linar combination
            python -m ibeis.dev --allgt -t \
                custom:fg_weight=0.0 \
            \
                custom:rrvsone_on=True,prior_coeff=1.0,unconstrained_coeff=0.0,fs_lnbnn_min=0.0,fs_lnbnn_max=1.0,nAnnotPerNameVsOne=200,nNameShortlistVsone=200 \
            \
                custom:rrvsone_on=True,prior_coeff=.5,unconstrained_coeff=0.5,fs_lnbnn_min=0.0,fs_lnbnn_max=1.0,nAnnotPerNameVsOne=200,nNameShortlistVsone=200 \
            \
              --db PZ_MTEST
            #--print-confusion-stats --print-gtscore
            #----
        
            # Testing no affine invaraiance and rotation invariance
            python -m ibeis.dev -t custom:AI=True,RI=True custom:AI=False,RI=True custom:AI=True,RI=False custom:AI=False,RI=False --db PZ_MTEST --show
        
        Caveats / Things we are not currently doing
        -------------------------------------------
        
        * We do not add or remove points from kdtrees. They are always rebuilt
        
        .. |CircleCI| image:: https://circleci.com/gh/Erotemic/ibeis.svg?style=svg
            :target: https://circleci.com/gh/Erotemic/ibeis
        .. |Travis| image:: https://img.shields.io/travis/Erotemic/ibeis/master.svg?label=Travis%20CI
           :target: https://travis-ci.org/Erotemic/ibeis?branch=master
        .. |Appveyor| image:: https://ci.appveyor.com/api/projects/status/github/Erotemic/ibeis?branch=master&svg=True
           :target: https://ci.appveyor.com/project/Erotemic/ibeis/branch/master
        .. |Codecov| image:: https://codecov.io/github/Erotemic/ibeis/badge.svg?branch=master&service=github
           :target: https://codecov.io/github/Erotemic/ibeis?branch=master
        .. |Pypi| image:: https://img.shields.io/pypi/v/ibeis.svg
           :target: https://pypi.python.org/pypi/ibeis
        .. |Downloads| image:: https://img.shields.io/pypi/dm/ibeis.svg
           :target: https://pypistats.org/packages/ibeis
        .. |ReadTheDocs| image:: https://readthedocs.org/projects/ibeis/badge/?version=latest
            :target: http://ibeis.readthedocs.io/en/latest/
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/x-rst
Provides-Extra: optional
Provides-Extra: tests
Provides-Extra: all
