Package: ibeis
This project is a component of the WildMe / WildBook project: Seehttps://github.com/WildbookOrg/NOTE: This IBEIS software is the result of my (Jon Crall’s) [PhD
work](https://github.com/Erotemic/crall-thesis-2017). After I graduated, the
image analysis components of IBEIS and the core HotSpotter program have been
transferred and are now being developed by the WildMe organization. While this
software is maintained and supported, it can only handle medium scale
populations and its it GUI interface can be difficult to work with. If you have
a larger population or the need for simpler and scalable web interfaces  please
reach out to the WildMe project atservices@wildme.org(more info:https://www.wildme.org/#/services/).IBEIS - Image AnalysisI.B.E.I.S. = Image Based Ecological Information SystemInstallation Instructions (updated 2020-Nov-01)The IBEIS software is now available onpypifor Linux systems. This means if you havePython installed. You can
simply run:pipinstallibeisto install the software. Then the command to run the GUI is:ibeisOn Windows / OSX I recommend using a Linux virtual machine. However, if you are
computer savvy it is possible to build all of the requirements on from source.
The only tricky components are installing the packages with binary
dependencies:pyhesaffandvtool_ibeis. If you have these built then
the rest of the dependencies can be installed from pypi even on OSX / Windows.NOTE: When using a VM on windows, you may encounter an error:qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in
... even though it was found. This application failed to start because no
Qt platform plugin could be initialized. Reinstalling the application may
fix this problem.

Available platform plugins are: xcb, eglfs, ...

Core dumpedThe reason the issue happens appears to be because the opencv-python package
includes libraries also packaged with PyQt5 and those are conflicting.The workaround is to uninstall opencv-python and then install a variant that
does not include extra Qt libs:pipuninstallopencv-pythonpipinstallopencv-python-headlessBasic Usage (updated 2020-Nov-01)After installation running theibeiscommand will open the GUI:If you have already made a database, it will automatically open the most recently used database.If this is the first time you’ve run the program it will not have a database opened:Select new database, (which will first ask you to select a work directory where all of your databases will live).
Then you will be asked to create a database name. Select one and then create the database in your work directory.You can drag and drop images into the GUI to add them to the database.  Double
clicking an image lets you add “annotations”:You can also right click one or more images and click “Add annotations from
entire images” if your images are already localized to a single individual.It important than when you add an annotation, you set its species. You can
right click multiple annotations and click “set annotation species”. Change
this to anything other than “____”.Once you have annotations with species, you can click one and press “q” to
query for matches in the database of other annotations:Right clicking and marking each match as “True” or “False” (or alternatively
selecting a row and pressing “T” or “F”) will mark images as the same or
different individuals. Groups marked as the same individual will appear in the
“Tree of Names”.Note there are also batch identification methods in the “ID Encounters” “ID
Exemplars” and “Advanced ID Interface” (my personal recommendation). Play
around with different right-click menus (although note that some of these are
buggy and will crash the program), but the main simple identification
procedures are robust and should not crash.Program DescriptionIBEIS 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 PyQt5 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/ibeisThe 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 ExecutablesUnfortunately we have not released self-installing-executables for IBEIS yet.
We ~plan~ hope to release these soon™.However there are old [HotSpotter](https://github.com/Erotemic/hotspotter) (the
predecessor to IBEIS) binaries available.Dropbox should still be hosting the download links:Win32 Installer:https://www.dropbox.com/s/5j1xyx2hq1wzqz2/hotspotter-win32-setup.exe?dl=0OSX Installer:https://www.dropbox.com/s/q0vzz3xnjbxhsda/hotspotter_installer_mac.dmg?dl=0IPFS CIDs for the previous installers are QmSnyetkniriHUwTxvzwhkysPKjUj7udBqq5mpK24VJXVM and QmZ3WknrAaxPZhZebdQWZ45EEKwu1Tr6bkFWJzfPRtENs7.If you are unfamiliar with IPFS use the following gateway links:https://ipfs.io/ipfs/QmSnyetkniriHUwTxvzwhkysPKjUj7udBqq5mpK24VJXVMhttps://ipfs.io/ipfs/QmZ3WknrAaxPZhZebdQWZ45EEKwu1Tr6bkFWJzfPRtENs7Visual DemoMatch ScoringSpatial Verificationpython-mvtool.spatial_verificationspatially_verify_kpts--showName Scoringpython-mibeis.algo.hots.chip_matchshow_single_namematch--qaid1--showIdentification Rankingpython-mibeis.algo.hots.chip_matchshow_ranked_matches--show--qaid86Inference# broken
# python -m ibeis.algo.preproc.preproc_encounter compute_encounter_groups --showInternal ModulesIn the interest of modular code we are actively developing several different modules.ibeisutoolplottool_ibeisguitool_ibeisdtool_ibeispyhesaffpyflann_ibeisvtool_ibeisfutures_actors—bluemellophone’s IBEIS Image Analysis moduleshttps://github.com/WildbookOrg/detecttoolshttps://github.com/WildbookOrg/pyrfdocs:http://bluemellophone.github.io/pyrfBuilding from sourceTo build from source you need to be able to build the following 3 projects with
binary dependences. These depened on having a development version of OpenCV and
LZ4.https://github.com/Erotemic/vtool_ibeis_exthttps://github.com/Erotemic/pyflann_ibeishttps://github.com/Erotemic/pyhesaffIf you are on Linux simply using the wheels for the above projects (
i.e.pip install vtool_ibeis_ext  pyflann_ibeis pyhesaffis recommended).
On OSX and Win32 these need to be build manually (any contributions to help
these build win32 or osx wheels on their respective project CI would be
amazing!).The rest of the dependency repos (guitool_ibeis,plottool_ibeis,dtool_ibeis,vtool_ibeis,)  are pure python and can be installed in
development mode with the normal clone the repo, and runpip install-e.inside the repo process.Given a Python environment where each of the dependency modules is installed
this repo can be installed withpip install-e.as well.Demo DatabasesA set of small (400MB) demo databases PZ_MTEST1 and NAUT_TEST can be downloaded
via.pythondev/reset_dbs.pyNote that it downloads the data from an IPFS gateway, which may be slow and
require several attempts before it works.Running TestsThe tests depend on an even smaller set of test databases, which can be
prepared viaibeis –reset-ci-dbs. Once you have the test data you can use
therun_doctests.shorrun_tests.pyscript to execute the system tests.Known issuesWe do not add or remove points from kdtrees. They are always rebuiltChanging algorithm settings in the preferences window seems bugged and
probably requires a fix in utool. The default settings should work and using
the Python API with explicit algorithm settings should also be fine.The code is a mess! PRs are welcome!The UI has lots of unused or broken components. PRs to disable or make these
nicer are welcome!The only blockers for Windows / OSX pip installs are pyhesaff, pyflann_ibeis, and vtool_ibeis_ext binary wheels. Getting these to build on Github Actions would mean pip installable IBEIS on non-Linux systems.Citations and Related WorkThe best citation for this work would bemy thesis.@phdthesis{crall_identifying_2017,address={Troy, NY},author={Crall, Jonathan P.},school={Department of Computer Science, Rensselaer Polytechnic Institute},title={Identifying {Individual} {Animals} using {Ranking}, {Verification}, and {Connectivity}},type={Ph.{D}. {Thesis}},year={2017}}The original HotSpotter paper is:Crall, Stewart, Bertger-Wolf, Rubenstein, and Sundaresan. “HotSpotter - Patterned Species Instance Recognition” WACV 2013Other relevant citations are:Parham, Jason. “Animal Detection for Photographic Censusing” RPI PhD Thesis 2021Weideman, Hendrik. “Contour-Based Instance Recognition of Animals” RPI PhD Thesis 2019Parham, Crall, Stewart, Berger-Wolf, and Rubenstein, “Animal population censusing at scale with citizen science and photographic identification” AAAI 2017