基于图像的生态信息系统
ibeis的Python项目详细描述
这个项目是WildMe/WildBook项目的一个组件：请参见https://github.com/WildbookOrg/
IBEIS-图像分析
一、 B.E.I.S.=基于图像的生态信息系统
程序说明
IBEIS图象和衍生数据的存储和管理程序 用于计算机视觉算法。它的目的是计算谁是动物，什么 动物是物种，动物的最终目标是 问重要的为什么是生物学问题。这张回购图像分析图片 IBEIS的分析模块。它既是python模块又是独立程序。在
目前，该系统是围绕和SQLite数据库构建的，一个pyqt4gui，以及 matplotlib可视化。使用的算法有：随机森林物种 检测定位，hessian仿射关键点检测，SIFT关键点 说明，使用近似近邻进行LNBNN识别。 正在开发的算法是用于识别的SMK（选择性匹配核） 以及用于检测和定位的深层神经网络。在
IBEIS的核心是IBEISController类。它为IBEIS提供了一个API 数据管理和算法。IBEIS API文档可在以下位置找到： <引用>http://erotemic.github.io/ibeis
ibeisgui（图形用户界面）构建在API之上。 我们也在尝试一种新的web前端，它绕过了旧的GUI代码。在
自行安装的可执行文件：
不幸的是，我们还没有发布IBEIS的自安装可执行文件。 我们计划“很快”发布这些。在
但是也有旧的热水獭（IBEIS基于的软件） 二进制文件可用。可从以下网址下载：http://cs.rpi.edu/hotspotter/
可视化演示
比赛得分
空间验证
python -m vtool.spatial_verification --test-spatially_verify_kpts --show
姓名评分
身份等级
python -m ibeis.algo.hots.chip_match show_ranked_matches --show --qaid 86推论
# broken
# python -m ibeis.algo.preproc.preproc_encounter compute_encounter_groups --show内部模块
为了对模块化代码感兴趣，我们正在积极开发几个不同的模块。在
Erotemic的IBEIS图像分析模块依赖关系
- 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的IBEIS图像分析模块
- https://github.com/WildbookOrg/detecttools
- https://github.com/WildbookOrg/pyrf 文件：http://bluemellophone.github.io/pyrf
IBEIS模块本身：
IBEIS开发环境设置
注：此部分已过时。在
# 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 exportCODE_DIR=~/code mkdir $CODE_DIRcd$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
运行测试
运行测试的新方法是使用xdoctest，或者使用“run_博士.sh“剧本。在
示例用法
（注：这份清单还远未完成）
#-------------------- # 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
注意事项/我们目前没有做的事情
- 我们不添加或删除kdtrees中的点。他们总是被重建
- 项目
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