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GNU General Public License |
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========================== |
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_Version 3, 29 June 2007_ |
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_Copyright © 2007 Free Software Foundation, Inc. <<http://fsf.org/>>_ |
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Everyone is permitted to copy and distribute verbatim copies of this license |
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document, but changing it is not allowed. |
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|
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## Preamble |
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|
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The GNU General Public License is a free, copyleft license for software and other |
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kinds of works. |
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|
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The licenses for most software and other practical works are designed to take away |
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your freedom to share and change the works. By contrast, the GNU General Public |
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License is intended to guarantee your freedom to share and change all versions of a |
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program--to make sure it remains free software for all its users. We, the Free |
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Software Foundation, use the GNU General Public License for most of our software; it |
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applies also to any other work released this way by its authors. You can apply it to |
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your programs, too. |
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|
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When we speak of free software, we are referring to freedom, not price. Our General |
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Public Licenses are designed to make sure that you have the freedom to distribute |
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copies of free software (and charge for them if you wish), that you receive source |
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code or can get it if you want it, that you can change the software or use pieces of |
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it in new free programs, and that you know you can do these things. |
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|
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To protect your rights, we need to prevent others from denying you these rights or |
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asking you to surrender the rights. Therefore, you have certain responsibilities if |
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you distribute copies of the software, or if you modify it: responsibilities to |
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respect the freedom of others. |
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|
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For example, if you distribute copies of such a program, whether gratis or for a fee, |
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you must pass on to the recipients the same freedoms that you received. You must make |
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sure that they, too, receive or can get the source code. And you must show them these |
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terms so they know their rights. |
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|
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Developers that use the GNU GPL protect your rights with two steps: **(1)** assert |
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copyright on the software, and **(2)** offer you this License giving you legal permission |
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to copy, distribute and/or modify it. |
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|
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For the developers' and authors' protection, the GPL clearly explains that there is |
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no warranty for this free software. For both users' and authors' sake, the GPL |
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requires that modified versions be marked as changed, so that their problems will not |
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be attributed erroneously to authors of previous versions. |
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|
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Some devices are designed to deny users access to install or run modified versions of |
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the software inside them, although the manufacturer can do so. This is fundamentally |
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incompatible with the aim of protecting users' freedom to change the software. The |
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systematic pattern of such abuse occurs in the area of products for individuals to |
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use, which is precisely where it is most unacceptable. Therefore, we have designed |
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this version of the GPL to prohibit the practice for those products. If such problems |
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arise substantially in other domains, we stand ready to extend this provision to |
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those domains in future versions of the GPL, as needed to protect the freedom of |
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users. |
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|
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Finally, every program is threatened constantly by software patents. States should |
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not allow patents to restrict development and use of software on general-purpose |
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computers, but in those that do, we wish to avoid the special danger that patents |
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applied to a free program could make it effectively proprietary. To prevent this, the |
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GPL assures that patents cannot be used to render the program non-free. |
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|
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The precise terms and conditions for copying, distribution and modification follow. |
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|
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## TERMS AND CONDITIONS |
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|
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### 0. Definitions |
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|
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“This License” refers to version 3 of the GNU General Public License. |
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|
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“Copyright” also means copyright-like laws that apply to other kinds of |
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works, such as semiconductor masks. |
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|
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“The Program” refers to any copyrightable work licensed under this |
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License. Each licensee is addressed as “you”. “Licensees” and |
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“recipients” may be individuals or organizations. |
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|
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To “modify” a work means to copy from or adapt all or part of the work in |
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a fashion requiring copyright permission, other than the making of an exact copy. The |
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resulting work is called a “modified version” of the earlier work or a |
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work “based on” the earlier work. |
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|
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A “covered work” means either the unmodified Program or a work based on |
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the Program. |
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|
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To “propagate” a work means to do anything with it that, without |
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permission, would make you directly or secondarily liable for infringement under |
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applicable copyright law, except executing it on a computer or modifying a private |
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copy. Propagation includes copying, distribution (with or without modification), |
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making available to the public, and in some countries other activities as well. |
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|
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To “convey” a work means any kind of propagation that enables other |
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parties to make or receive copies. Mere interaction with a user through a computer |
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network, with no transfer of a copy, is not conveying. |
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|
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An interactive user interface displays “Appropriate Legal Notices” to the |
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extent that it includes a convenient and prominently visible feature that **(1)** |
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displays an appropriate copyright notice, and **(2)** tells the user that there is no |
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warranty for the work (except to the extent that warranties are provided), that |
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licensees may convey the work under this License, and how to view a copy of this |
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License. If the interface presents a list of user commands or options, such as a |
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menu, a prominent item in the list meets this criterion. |
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|
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### 1. Source Code |
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|
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The “source code” for a work means the preferred form of the work for |
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making modifications to it. “Object code” means any non-source form of a |
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work. |
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|
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A “Standard Interface” means an interface that either is an official |
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standard defined by a recognized standards body, or, in the case of interfaces |
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specified for a particular programming language, one that is widely used among |
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developers working in that language. |
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|
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The “System Libraries” of an executable work include anything, other than |
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the work as a whole, that **(a)** is included in the normal form of packaging a Major |
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Component, but which is not part of that Major Component, and **(b)** serves only to |
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enable use of the work with that Major Component, or to implement a Standard |
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Interface for which an implementation is available to the public in source code form. |
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A “Major Component”, in this context, means a major essential component |
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(kernel, window system, and so on) of the specific operating system (if any) on which |
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the executable work runs, or a compiler used to produce the work, or an object code |
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interpreter used to run it. |
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|
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The “Corresponding Source” for a work in object code form means all the |
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source code needed to generate, install, and (for an executable work) run the object |
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code and to modify the work, including scripts to control those activities. However, |
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it does not include the work's System Libraries, or general-purpose tools or |
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generally available free programs which are used unmodified in performing those |
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activities but which are not part of the work. For example, Corresponding Source |
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includes interface definition files associated with source files for the work, and |
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the source code for shared libraries and dynamically linked subprograms that the work |
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is specifically designed to require, such as by intimate data communication or |
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control flow between those subprograms and other parts of the work. |
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|
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The Corresponding Source need not include anything that users can regenerate |
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automatically from other parts of the Corresponding Source. |
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|
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The Corresponding Source for a work in source code form is that same work. |
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|
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### 2. Basic Permissions |
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|
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All rights granted under this License are granted for the term of copyright on the |
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Program, and are irrevocable provided the stated conditions are met. This License |
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explicitly affirms your unlimited permission to run the unmodified Program. The |
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output from running a covered work is covered by this License only if the output, |
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given its content, constitutes a covered work. This License acknowledges your rights |
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of fair use or other equivalent, as provided by copyright law. |
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|
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You may make, run and propagate covered works that you do not convey, without |
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conditions so long as your license otherwise remains in force. You may convey covered |
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works to others for the sole purpose of having them make modifications exclusively |
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for you, or provide you with facilities for running those works, provided that you |
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comply with the terms of this License in conveying all material for which you do not |
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control copyright. Those thus making or running the covered works for you must do so |
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exclusively on your behalf, under your direction and control, on terms that prohibit |
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them from making any copies of your copyrighted material outside their relationship |
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with you. |
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|
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Conveying under any other circumstances is permitted solely under the conditions |
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stated below. Sublicensing is not allowed; section 10 makes it unnecessary. |
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|
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### 3. Protecting Users' Legal Rights From Anti-Circumvention Law |
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|
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No covered work shall be deemed part of an effective technological measure under any |
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applicable law fulfilling obligations under article 11 of the WIPO copyright treaty |
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adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention |
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of such measures. |
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|
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When you convey a covered work, you waive any legal power to forbid circumvention of |
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technological measures to the extent such circumvention is effected by exercising |
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rights under this License with respect to the covered work, and you disclaim any |
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intention to limit operation or modification of the work as a means of enforcing, |
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against the work's users, your or third parties' legal rights to forbid circumvention |
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of technological measures. |
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|
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### 4. Conveying Verbatim Copies |
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|
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You may convey verbatim copies of the Program's source code as you receive it, in any |
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medium, provided that you conspicuously and appropriately publish on each copy an |
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appropriate copyright notice; keep intact all notices stating that this License and |
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any non-permissive terms added in accord with section 7 apply to the code; keep |
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intact all notices of the absence of any warranty; and give all recipients a copy of |
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this License along with the Program. |
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|
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You may charge any price or no price for each copy that you convey, and you may offer |
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support or warranty protection for a fee. |
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|
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### 5. Conveying Modified Source Versions |
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|
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You may convey a work based on the Program, or the modifications to produce it from |
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the Program, in the form of source code under the terms of section 4, provided that |
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you also meet all of these conditions: |
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|
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* **a)** The work must carry prominent notices stating that you modified it, and giving a |
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relevant date. |
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* **b)** The work must carry prominent notices stating that it is released under this |
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License and any conditions added under section 7. This requirement modifies the |
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requirement in section 4 to “keep intact all notices”. |
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* **c)** You must license the entire work, as a whole, under this License to anyone who |
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comes into possession of a copy. This License will therefore apply, along with any |
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applicable section 7 additional terms, to the whole of the work, and all its parts, |
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regardless of how they are packaged. This License gives no permission to license the |
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work in any other way, but it does not invalidate such permission if you have |
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separately received it. |
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* **d)** If the work has interactive user interfaces, each must display Appropriate Legal |
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Notices; however, if the Program has interactive interfaces that do not display |
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Appropriate Legal Notices, your work need not make them do so. |
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|
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A compilation of a covered work with other separate and independent works, which are |
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not by their nature extensions of the covered work, and which are not combined with |
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it such as to form a larger program, in or on a volume of a storage or distribution |
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medium, is called an “aggregate” if the compilation and its resulting |
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copyright are not used to limit the access or legal rights of the compilation's users |
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beyond what the individual works permit. Inclusion of a covered work in an aggregate |
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does not cause this License to apply to the other parts of the aggregate. |
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|
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### 6. Conveying Non-Source Forms |
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|
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You may convey a covered work in object code form under the terms of sections 4 and |
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5, provided that you also convey the machine-readable Corresponding Source under the |
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terms of this License, in one of these ways: |
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|
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* **a)** Convey the object code in, or embodied in, a physical product (including a |
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physical distribution medium), accompanied by the Corresponding Source fixed on a |
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durable physical medium customarily used for software interchange. |
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* **b)** Convey the object code in, or embodied in, a physical product (including a |
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physical distribution medium), accompanied by a written offer, valid for at least |
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three years and valid for as long as you offer spare parts or customer support for |
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that product model, to give anyone who possesses the object code either **(1)** a copy of |
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the Corresponding Source for all the software in the product that is covered by this |
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License, on a durable physical medium customarily used for software interchange, for |
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a price no more than your reasonable cost of physically performing this conveying of |
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source, or **(2)** access to copy the Corresponding Source from a network server at no |
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charge. |
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* **c)** Convey individual copies of the object code with a copy of the written offer to |
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provide the Corresponding Source. This alternative is allowed only occasionally and |
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noncommercially, and only if you received the object code with such an offer, in |
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accord with subsection 6b. |
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* **d)** Convey the object code by offering access from a designated place (gratis or for |
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a charge), and offer equivalent access to the Corresponding Source in the same way |
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through the same place at no further charge. You need not require recipients to copy |
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the Corresponding Source along with the object code. If the place to copy the object |
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code is a network server, the Corresponding Source may be on a different server |
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(operated by you or a third party) that supports equivalent copying facilities, |
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provided you maintain clear directions next to the object code saying where to find |
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the Corresponding Source. Regardless of what server hosts the Corresponding Source, |
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you remain obligated to ensure that it is available for as long as needed to satisfy |
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these requirements. |
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* **e)** Convey the object code using peer-to-peer transmission, provided you inform |
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other peers where the object code and Corresponding Source of the work are being |
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offered to the general public at no charge under subsection 6d. |
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|
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A separable portion of the object code, whose source code is excluded from the |
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Corresponding Source as a System Library, need not be included in conveying the |
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object code work. |
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|
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A “User Product” is either **(1)** a “consumer product”, which |
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means any tangible personal property which is normally used for personal, family, or |
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household purposes, or **(2)** anything designed or sold for incorporation into a |
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dwelling. In determining whether a product is a consumer product, doubtful cases |
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shall be resolved in favor of coverage. For a particular product received by a |
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particular user, “normally used” refers to a typical or common use of |
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that class of product, regardless of the status of the particular user or of the way |
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in which the particular user actually uses, or expects or is expected to use, the |
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product. A product is a consumer product regardless of whether the product has |
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substantial commercial, industrial or non-consumer uses, unless such uses represent |
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the only significant mode of use of the product. |
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|
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“Installation Information” for a User Product means any methods, |
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procedures, authorization keys, or other information required to install and execute |
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modified versions of a covered work in that User Product from a modified version of |
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its Corresponding Source. The information must suffice to ensure that the continued |
|||
functioning of the modified object code is in no case prevented or interfered with |
|||
solely because modification has been made. |
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|
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If you convey an object code work under this section in, or with, or specifically for |
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use in, a User Product, and the conveying occurs as part of a transaction in which |
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the right of possession and use of the User Product is transferred to the recipient |
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in perpetuity or for a fixed term (regardless of how the transaction is |
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characterized), the Corresponding Source conveyed under this section must be |
|||
accompanied by the Installation Information. But this requirement does not apply if |
|||
neither you nor any third party retains the ability to install modified object code |
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on the User Product (for example, the work has been installed in ROM). |
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|
|||
The requirement to provide Installation Information does not include a requirement to |
|||
continue to provide support service, warranty, or updates for a work that has been |
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modified or installed by the recipient, or for the User Product in which it has been |
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modified or installed. Access to a network may be denied when the modification itself |
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materially and adversely affects the operation of the network or violates the rules |
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and protocols for communication across the network. |
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|
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Corresponding Source conveyed, and Installation Information provided, in accord with |
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this section must be in a format that is publicly documented (and with an |
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implementation available to the public in source code form), and must require no |
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special password or key for unpacking, reading or copying. |
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|
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### 7. Additional Terms |
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|
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“Additional permissions” are terms that supplement the terms of this |
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License by making exceptions from one or more of its conditions. Additional |
|||
permissions that are applicable to the entire Program shall be treated as though they |
|||
were included in this License, to the extent that they are valid under applicable |
|||
law. If additional permissions apply only to part of the Program, that part may be |
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used separately under those permissions, but the entire Program remains governed by |
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this License without regard to the additional permissions. |
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|
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When you convey a copy of a covered work, you may at your option remove any |
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additional permissions from that copy, or from any part of it. (Additional |
|||
permissions may be written to require their own removal in certain cases when you |
|||
modify the work.) You may place additional permissions on material, added by you to a |
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covered work, for which you have or can give appropriate copyright permission. |
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|
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Notwithstanding any other provision of this License, for material you add to a |
|||
covered work, you may (if authorized by the copyright holders of that material) |
|||
supplement the terms of this License with terms: |
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|
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* **a)** Disclaiming warranty or limiting liability differently from the terms of |
|||
sections 15 and 16 of this License; or |
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* **b)** Requiring preservation of specified reasonable legal notices or author |
|||
attributions in that material or in the Appropriate Legal Notices displayed by works |
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containing it; or |
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* **c)** Prohibiting misrepresentation of the origin of that material, or requiring that |
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modified versions of such material be marked in reasonable ways as different from the |
|||
original version; or |
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* **d)** Limiting the use for publicity purposes of names of licensors or authors of the |
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material; or |
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* **e)** Declining to grant rights under trademark law for use of some trade names, |
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trademarks, or service marks; or |
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* **f)** Requiring indemnification of licensors and authors of that material by anyone |
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who conveys the material (or modified versions of it) with contractual assumptions of |
|||
liability to the recipient, for any liability that these contractual assumptions |
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directly impose on those licensors and authors. |
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|
|||
All other non-permissive additional terms are considered “further |
|||
restrictions” within the meaning of section 10. If the Program as you received |
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it, or any part of it, contains a notice stating that it is governed by this License |
|||
along with a term that is a further restriction, you may remove that term. If a |
|||
license document contains a further restriction but permits relicensing or conveying |
|||
under this License, you may add to a covered work material governed by the terms of |
|||
that license document, provided that the further restriction does not survive such |
|||
relicensing or conveying. |
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|
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If you add terms to a covered work in accord with this section, you must place, in |
|||
the relevant source files, a statement of the additional terms that apply to those |
|||
files, or a notice indicating where to find the applicable terms. |
|||
|
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Additional terms, permissive or non-permissive, may be stated in the form of a |
|||
separately written license, or stated as exceptions; the above requirements apply |
|||
either way. |
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|
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### 8. Termination |
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|
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You may not propagate or modify a covered work except as expressly provided under |
|||
this License. Any attempt otherwise to propagate or modify it is void, and will |
|||
automatically terminate your rights under this License (including any patent licenses |
|||
granted under the third paragraph of section 11). |
|||
|
|||
However, if you cease all violation of this License, then your license from a |
|||
particular copyright holder is reinstated **(a)** provisionally, unless and until the |
|||
copyright holder explicitly and finally terminates your license, and **(b)** permanently, |
|||
if the copyright holder fails to notify you of the violation by some reasonable means |
|||
prior to 60 days after the cessation. |
|||
|
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Moreover, your license from a particular copyright holder is reinstated permanently |
|||
if the copyright holder notifies you of the violation by some reasonable means, this |
|||
is the first time you have received notice of violation of this License (for any |
|||
work) from that copyright holder, and you cure the violation prior to 30 days after |
|||
your receipt of the notice. |
|||
|
|||
Termination of your rights under this section does not terminate the licenses of |
|||
parties who have received copies or rights from you under this License. If your |
|||
rights have been terminated and not permanently reinstated, you do not qualify to |
|||
receive new licenses for the same material under section 10. |
|||
|
|||
### 9. Acceptance Not Required for Having Copies |
|||
|
|||
You are not required to accept this License in order to receive or run a copy of the |
|||
Program. Ancillary propagation of a covered work occurring solely as a consequence of |
|||
using peer-to-peer transmission to receive a copy likewise does not require |
|||
acceptance. However, nothing other than this License grants you permission to |
|||
propagate or modify any covered work. These actions infringe copyright if you do not |
|||
accept this License. Therefore, by modifying or propagating a covered work, you |
|||
indicate your acceptance of this License to do so. |
|||
|
|||
### 10. Automatic Licensing of Downstream Recipients |
|||
|
|||
Each time you convey a covered work, the recipient automatically receives a license |
|||
from the original licensors, to run, modify and propagate that work, subject to this |
|||
License. You are not responsible for enforcing compliance by third parties with this |
|||
License. |
|||
|
|||
An “entity transaction” is a transaction transferring control of an |
|||
organization, or substantially all assets of one, or subdividing an organization, or |
|||
merging organizations. If propagation of a covered work results from an entity |
|||
transaction, each party to that transaction who receives a copy of the work also |
|||
receives whatever licenses to the work the party's predecessor in interest had or |
|||
could give under the previous paragraph, plus a right to possession of the |
|||
Corresponding Source of the work from the predecessor in interest, if the predecessor |
|||
has it or can get it with reasonable efforts. |
|||
|
|||
You may not impose any further restrictions on the exercise of the rights granted or |
|||
affirmed under this License. For example, you may not impose a license fee, royalty, |
|||
or other charge for exercise of rights granted under this License, and you may not |
|||
initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging |
|||
that any patent claim is infringed by making, using, selling, offering for sale, or |
|||
importing the Program or any portion of it. |
|||
|
|||
### 11. Patents |
|||
|
|||
A “contributor” is a copyright holder who authorizes use under this |
|||
License of the Program or a work on which the Program is based. The work thus |
|||
licensed is called the contributor's “contributor version”. |
|||
|
|||
A contributor's “essential patent claims” are all patent claims owned or |
|||
controlled by the contributor, whether already acquired or hereafter acquired, that |
|||
would be infringed by some manner, permitted by this License, of making, using, or |
|||
selling its contributor version, but do not include claims that would be infringed |
|||
only as a consequence of further modification of the contributor version. For |
|||
purposes of this definition, “control” includes the right to grant patent |
|||
sublicenses in a manner consistent with the requirements of this License. |
|||
|
|||
Each contributor grants you a non-exclusive, worldwide, royalty-free patent license |
|||
under the contributor's essential patent claims, to make, use, sell, offer for sale, |
|||
import and otherwise run, modify and propagate the contents of its contributor |
|||
version. |
|||
|
|||
In the following three paragraphs, a “patent license” is any express |
|||
agreement or commitment, however denominated, not to enforce a patent (such as an |
|||
express permission to practice a patent or covenant not to sue for patent |
|||
infringement). To “grant” such a patent license to a party means to make |
|||
such an agreement or commitment not to enforce a patent against the party. |
|||
|
|||
If you convey a covered work, knowingly relying on a patent license, and the |
|||
Corresponding Source of the work is not available for anyone to copy, free of charge |
|||
and under the terms of this License, through a publicly available network server or |
|||
other readily accessible means, then you must either **(1)** cause the Corresponding |
|||
Source to be so available, or **(2)** arrange to deprive yourself of the benefit of the |
|||
patent license for this particular work, or **(3)** arrange, in a manner consistent with |
|||
the requirements of this License, to extend the patent license to downstream |
|||
recipients. “Knowingly relying” means you have actual knowledge that, but |
|||
for the patent license, your conveying the covered work in a country, or your |
|||
recipient's use of the covered work in a country, would infringe one or more |
|||
identifiable patents in that country that you have reason to believe are valid. |
|||
|
|||
If, pursuant to or in connection with a single transaction or arrangement, you |
|||
convey, or propagate by procuring conveyance of, a covered work, and grant a patent |
|||
license to some of the parties receiving the covered work authorizing them to use, |
|||
propagate, modify or convey a specific copy of the covered work, then the patent |
|||
license you grant is automatically extended to all recipients of the covered work and |
|||
works based on it. |
|||
|
|||
A patent license is “discriminatory” if it does not include within the |
|||
scope of its coverage, prohibits the exercise of, or is conditioned on the |
|||
non-exercise of one or more of the rights that are specifically granted under this |
|||
License. You may not convey a covered work if you are a party to an arrangement with |
|||
a third party that is in the business of distributing software, under which you make |
|||
payment to the third party based on the extent of your activity of conveying the |
|||
work, and under which the third party grants, to any of the parties who would receive |
|||
the covered work from you, a discriminatory patent license **(a)** in connection with |
|||
copies of the covered work conveyed by you (or copies made from those copies), or **(b)** |
|||
primarily for and in connection with specific products or compilations that contain |
|||
the covered work, unless you entered into that arrangement, or that patent license |
|||
was granted, prior to 28 March 2007. |
|||
|
|||
Nothing in this License shall be construed as excluding or limiting any implied |
|||
license or other defenses to infringement that may otherwise be available to you |
|||
under applicable patent law. |
|||
|
|||
### 12. No Surrender of Others' Freedom |
|||
|
|||
If conditions are imposed on you (whether by court order, agreement or otherwise) |
|||
that contradict the conditions of this License, they do not excuse you from the |
|||
conditions of this License. If you cannot convey a covered work so as to satisfy |
|||
simultaneously your obligations under this License and any other pertinent |
|||
obligations, then as a consequence you may not convey it at all. For example, if you |
|||
agree to terms that obligate you to collect a royalty for further conveying from |
|||
those to whom you convey the Program, the only way you could satisfy both those terms |
|||
and this License would be to refrain entirely from conveying the Program. |
|||
|
|||
### 13. Use with the GNU Affero General Public License |
|||
|
|||
Notwithstanding any other provision of this License, you have permission to link or |
|||
combine any covered work with a work licensed under version 3 of the GNU Affero |
|||
General Public License into a single combined work, and to convey the resulting work. |
|||
The terms of this License will continue to apply to the part which is the covered |
|||
work, but the special requirements of the GNU Affero General Public License, section |
|||
13, concerning interaction through a network will apply to the combination as such. |
|||
|
|||
### 14. Revised Versions of this License |
|||
|
|||
The Free Software Foundation may publish revised and/or new versions of the GNU |
|||
General Public License from time to time. Such new versions will be similar in spirit |
|||
to the present version, but may differ in detail to address new problems or concerns. |
|||
|
|||
Each version is given a distinguishing version number. If the Program specifies that |
|||
a certain numbered version of the GNU General Public License “or any later |
|||
version” applies to it, you have the option of following the terms and |
|||
conditions either of that numbered version or of any later version published by the |
|||
Free Software Foundation. If the Program does not specify a version number of the GNU |
|||
General Public License, you may choose any version ever published by the Free |
|||
Software Foundation. |
|||
|
|||
If the Program specifies that a proxy can decide which future versions of the GNU |
|||
General Public License can be used, that proxy's public statement of acceptance of a |
|||
version permanently authorizes you to choose that version for the Program. |
|||
|
|||
Later license versions may give you additional or different permissions. However, no |
|||
additional obligations are imposed on any author or copyright holder as a result of |
|||
your choosing to follow a later version. |
|||
|
|||
### 15. Disclaimer of Warranty |
|||
|
|||
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. |
|||
EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES |
|||
PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER |
|||
EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF |
|||
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE |
|||
QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE |
|||
DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. |
|||
|
|||
### 16. Limitation of Liability |
|||
|
|||
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY |
|||
COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS |
|||
PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, |
|||
INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE |
|||
PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE |
|||
OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE |
|||
WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE |
|||
POSSIBILITY OF SUCH DAMAGES. |
|||
|
|||
### 17. Interpretation of Sections 15 and 16 |
|||
|
|||
If the disclaimer of warranty and limitation of liability provided above cannot be |
|||
given local legal effect according to their terms, reviewing courts shall apply local |
|||
law that most closely approximates an absolute waiver of all civil liability in |
|||
connection with the Program, unless a warranty or assumption of liability accompanies |
|||
a copy of the Program in return for a fee. |
|||
|
|||
_END OF TERMS AND CONDITIONS_ |
|||
|
|||
## How to Apply These Terms to Your New Programs |
|||
|
|||
If you develop a new program, and you want it to be of the greatest possible use to |
|||
the public, the best way to achieve this is to make it free software which everyone |
|||
can redistribute and change under these terms. |
|||
|
|||
To do so, attach the following notices to the program. It is safest to attach them |
|||
to the start of each source file to most effectively state the exclusion of warranty; |
|||
and each file should have at least the “copyright” line and a pointer to |
|||
where the full notice is found. |
|||
|
|||
<one line to give the program's name and a brief idea of what it does.> |
|||
Copyright (C) 2020 Bob Rudis |
|||
|
|||
This program is free software: you can redistribute it and/or modify |
|||
it under the terms of the GNU General Public License as published by |
|||
the Free Software Foundation, either version 3 of the License, or |
|||
(at your option) any later version. |
|||
|
|||
This program is distributed in the hope that it will be useful, |
|||
but WITHOUT ANY WARRANTY; without even the implied warranty of |
|||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
|||
GNU General Public License for more details. |
|||
|
|||
You should have received a copy of the GNU General Public License |
|||
along with this program. If not, see <http://www.gnu.org/licenses/>. |
|||
|
|||
Also add information on how to contact you by electronic and paper mail. |
|||
|
|||
If the program does terminal interaction, make it output a short notice like this |
|||
when it starts in an interactive mode: |
|||
|
|||
lizzard Copyright (C) 2020 Bob Rudis |
|||
This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. |
|||
This is free software, and you are welcome to redistribute it |
|||
under certain conditions; type 'show c' for details. |
|||
|
|||
The hypothetical commands `show w` and `show c` should show the appropriate parts of |
|||
the General Public License. Of course, your program's commands might be different; |
|||
for a GUI interface, you would use an “about box”. |
|||
|
|||
You should also get your employer (if you work as a programmer) or school, if any, to |
|||
sign a “copyright disclaimer” for the program, if necessary. For more |
|||
information on this, and how to apply and follow the GNU GPL, see |
|||
<<http://www.gnu.org/licenses/>>. |
|||
|
|||
The GNU General Public License does not permit incorporating your program into |
|||
proprietary programs. If your program is a subroutine library, you may consider it |
|||
more useful to permit linking proprietary applications with the library. If this is |
|||
what you want to do, use the GNU Lesser General Public License instead of this |
|||
License. But first, please read |
|||
<<http://www.gnu.org/philosophy/why-not-lgpl.html>>. |
@ -1,4 +1,9 @@ |
|||
# Generated by roxygen2: do not edit by hand |
|||
|
|||
import(httr) |
|||
importFrom(jsonlite,fromJSON) |
|||
S3method(as.character,lzjd_hash) |
|||
S3method(print,lzjd_hash) |
|||
export(as_lzjd_hash) |
|||
export(compute_distance) |
|||
export(compute_similarity) |
|||
export(min_hash_for_file) |
|||
import(rJava) |
|||
|
@ -1,9 +1,12 @@ |
|||
#' ... |
|||
#' |
|||
#' Compute and Compare Lempel-Ziv Jaccard (LZJD) Similarity Hashes |
|||
#' |
|||
#' The Lempel-Ziv Jaccard Distance (LZJD) is a method to measure the similarity between binary byte sequences. |
|||
#' Tools are provided that wrap Java methods by Raff et al, (2017) <arXiv:1708.03346v2> for computing |
|||
#' and comparing LZJD hashes. |
|||
#' |
|||
#' @md |
|||
#' @name lizzard |
|||
#' @keywords internal |
|||
#' @author Bob Rudis (bob@@rud.is) |
|||
#' @import httr |
|||
#' @importFrom jsonlite fromJSON |
|||
#' @import rJava |
|||
"_PACKAGE" |
|||
|
@ -0,0 +1,100 @@ |
|||
#' Compute the LZJD hash for a file |
|||
#' |
|||
#' @param path path to file (it will be [path.expand()]ed). |
|||
#' @return a `lzjd_hash` object which corresponds to a `jsat.classifiers.DataPoint` |
|||
#' (<https://github.com/EdwardRaff/JSAT/blob/master/JSAT/src/jsat/classifiers/DataPoint.java)> |
|||
#' object which, in this case, is an integer vector. |
|||
#' @export |
|||
#' @examples |
|||
#' h1 <- min_hash_for_file(system.file("extdat", "index.html", package = "lizzard")) |
|||
min_hash_for_file <- function(path) { |
|||
|
|||
path <- path.expand(path[1]) |
|||
stopifnot(file.exists(path)) |
|||
|
|||
jlzjdf <- J("com.edwardraff.jlzjd.LZJDf") |
|||
File <- J("java.io.File") |
|||
|
|||
res <- jlzjdf$getMHforFile(.jnew(File, path)) |
|||
|
|||
class(res) <- c("lzjd_hash") |
|||
|
|||
res |
|||
|
|||
} |
|||
|
|||
#' Compute the similarity between two LZJD hashes |
|||
#' |
|||
#' @param h1,h2 LZJD hashes |
|||
#' @return numeric similarity value (0-1) |
|||
#' @export |
|||
compute_similarity <- function(h1, h2) { |
|||
|
|||
stopifnot(inherits(h1, "lzjd_hash")) |
|||
stopifnot(inherits(h2, "lzjd_hash")) |
|||
|
|||
jlzjdf <- J("com.edwardraff.jlzjd.LZJDf") |
|||
|
|||
jlzjdf$similarity(unclass(h1), unclass(h2)) |
|||
|
|||
} |
|||
|
|||
#' Compute the distance between two LZJD hashes |
|||
#' |
|||
#' @param h1,h2 LZJD hashes |
|||
#' @return numeric distance value (0-1) |
|||
#' @export |
|||
compute_distance <- function(h1, h2) { |
|||
|
|||
stopifnot(inherits(h1, "lzjd_hash")) |
|||
stopifnot(inherits(h2, "lzjd_hash")) |
|||
|
|||
jlzjdf <- J("com.edwardraff.jlzjd.LZJDf") |
|||
|
|||
jlzjdf$dist(unclass(h1), unclass(h2)) |
|||
|
|||
} |
|||
|
|||
#' @rdname min_hash_for_file |
|||
#' @param x, an `lzhd_hash` object |
|||
#' @param ... ignored |
|||
#' @export |
|||
print.lzjd_hash <- function(x, ...) { |
|||
cat("<lzjd_hash>") |
|||
} |
|||
|
|||
#' Turn an `lzhd_hash` object into a base 64 encoded string |
|||
#' |
|||
#' @param x, an `lzhd_hash` object |
|||
#' @param ... ignored |
|||
#' @return character |
|||
#' @export |
|||
as.character.lzjd_hash <- function(x, ...) { |
|||
|
|||
jlzjdf <- J("com.edwardraff.jlzjd.LZJDf") |
|||
ret <- jlzjdf$toBase64(unclass(x)) |
|||
if (ret == "") NA_character_ else ret |
|||
|
|||
} |
|||
|
|||
#' Turn an base 64 encoded LZJD hash into an `lzjd_hash` object |
|||
#' |
|||
#' @param x base 64 encoded LZJD |
|||
#' @return `lzjd_hash` |
|||
#' @export |
|||
as_lzjd_hash <- function(x) { |
|||
|
|||
x <- x[1] |
|||
stopifnot(is.character(x)) |
|||
|
|||
jlzjdf <- J("com.edwardraff.jlzjd.LZJDf") |
|||
ret <- jlzjdf$fromBase64(x) |
|||
if (length(ret)) { |
|||
class(ret) <- c("lzjd_hash") |
|||
ret |
|||
} else { |
|||
return(NULL) |
|||
} |
|||
|
|||
} |
|||
|
@ -0,0 +1,4 @@ |
|||
.onLoad <- function(libname, pkgname) { |
|||
rJava::.jpackage(pkgname, jars = "*", lib.loc = libname) |
|||
rJava::.jaddClassPath(dir(file.path(getwd(), "inst/java"), full.names = TRUE)) |
|||
} |
File diff suppressed because one or more lines are too long
File diff suppressed because it is too large
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
@ -1,4 +1,43 @@ |
|||
|
|||
# Placeholder with simple test |
|||
expect_equal(1 + 1, 2) |
|||
(h1 <- min_hash_for_file(system.file("extdat", "index.html", package = "lizzard"))) |
|||
(h2 <- min_hash_for_file(system.file("extdat", "index1.html", package = "lizzard"))) |
|||
(h3 <- min_hash_for_file(system.file("extdat", "index2.html", package = "lizzard"))) |
|||
(h4 <- min_hash_for_file(system.file("extdat", "RMacOSX-FAQ.html", package = "lizzard"))) |
|||
|
|||
expect_true(is.character(as.character(h4))) |
|||
|
|||
expect_true(is.integer(as_lzjd_hash(as.character(h4)))) |
|||
|
|||
expect_identical(as_lzjd_hash(as.character(h4)), h4) |
|||
|
|||
expect_equal(compute_similarity(h1, h1), 1) |
|||
|
|||
compute_similarity(h1, h2) |
|||
|
|||
compute_similarity(h1, h3) |
|||
|
|||
compute_similarity(h1, h4) |
|||
|
|||
compute_similarity(h2, h3) |
|||
|
|||
compute_similarity(h2, h4) |
|||
|
|||
compute_similarity(h3, h4) |
|||
|
|||
|
|||
expect_equal(compute_distance(h1, h1), 0) |
|||
|
|||
compute_distance(h1, h2) |
|||
|
|||
compute_distance(h1, h3) |
|||
|
|||
compute_distance(h1, h4) |
|||
|
|||
compute_distance(h2, h3) |
|||
|
|||
compute_distance(h2, h4) |
|||
|
|||
compute_distance(h3, h4) |
|||
|
|||
|
|||
|
|||
|
@ -0,0 +1,674 @@ |
|||
GNU GENERAL PUBLIC LICENSE |
|||
Version 3, 29 June 2007 |
|||
|
|||
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> |
|||
Everyone is permitted to copy and distribute verbatim copies |
|||
of this license document, but changing it is not allowed. |
|||
|
|||
Preamble |
|||
|
|||
The GNU General Public License is a free, copyleft license for |
|||
software and other kinds of works. |
|||
|
|||
The licenses for most software and other practical works are designed |
|||
to take away your freedom to share and change the works. By contrast, |
|||
the GNU General Public License is intended to guarantee your freedom to |
|||
share and change all versions of a program--to make sure it remains free |
|||
software for all its users. We, the Free Software Foundation, use the |
|||
GNU General Public License for most of our software; it applies also to |
|||
any other work released this way by its authors. You can apply it to |
|||
your programs, too. |
|||
|
|||
When we speak of free software, we are referring to freedom, not |
|||
price. Our General Public Licenses are designed to make sure that you |
|||
have the freedom to distribute copies of free software (and charge for |
|||
them if you wish), that you receive source code or can get it if you |
|||
want it, that you can change the software or use pieces of it in new |
|||
free programs, and that you know you can do these things. |
|||
|
|||
To protect your rights, we need to prevent others from denying you |
|||
these rights or asking you to surrender the rights. Therefore, you have |
|||
certain responsibilities if you distribute copies of the software, or if |
|||
you modify it: responsibilities to respect the freedom of others. |
|||
|
|||
For example, if you distribute copies of such a program, whether |
|||
gratis or for a fee, you must pass on to the recipients the same |
|||
freedoms that you received. You must make sure that they, too, receive |
|||
or can get the source code. And you must show them these terms so they |
|||
know their rights. |
|||
|
|||
Developers that use the GNU GPL protect your rights with two steps: |
|||
(1) assert copyright on the software, and (2) offer you this License |
|||
giving you legal permission to copy, distribute and/or modify it. |
|||
|
|||
For the developers' and authors' protection, the GPL clearly explains |
|||
that there is no warranty for this free software. For both users' and |
|||
authors' sake, the GPL requires that modified versions be marked as |
|||
changed, so that their problems will not be attributed erroneously to |
|||
authors of previous versions. |
|||
|
|||
Some devices are designed to deny users access to install or run |
|||
modified versions of the software inside them, although the manufacturer |
|||
can do so. This is fundamentally incompatible with the aim of |
|||
protecting users' freedom to change the software. The systematic |
|||
pattern of such abuse occurs in the area of products for individuals to |
|||
use, which is precisely where it is most unacceptable. Therefore, we |
|||
have designed this version of the GPL to prohibit the practice for those |
|||
products. If such problems arise substantially in other domains, we |
|||
stand ready to extend this provision to those domains in future versions |
|||
of the GPL, as needed to protect the freedom of users. |
|||
|
|||
Finally, every program is threatened constantly by software patents. |
|||
States should not allow patents to restrict development and use of |
|||
software on general-purpose computers, but in those that do, we wish to |
|||
avoid the special danger that patents applied to a free program could |
|||
make it effectively proprietary. To prevent this, the GPL assures that |
|||
patents cannot be used to render the program non-free. |
|||
|
|||
The precise terms and conditions for copying, distribution and |
|||
modification follow. |
|||
|
|||
TERMS AND CONDITIONS |
|||
|
|||
0. Definitions. |
|||
|
|||
"This License" refers to version 3 of the GNU General Public License. |
|||
|
|||
"Copyright" also means copyright-like laws that apply to other kinds of |
|||
works, such as semiconductor masks. |
|||
|
|||
"The Program" refers to any copyrightable work licensed under this |
|||
License. Each licensee is addressed as "you". "Licensees" and |
|||
"recipients" may be individuals or organizations. |
|||
|
|||
To "modify" a work means to copy from or adapt all or part of the work |
|||
in a fashion requiring copyright permission, other than the making of an |
|||
exact copy. The resulting work is called a "modified version" of the |
|||
earlier work or a work "based on" the earlier work. |
|||
|
|||
A "covered work" means either the unmodified Program or a work based |
|||
on the Program. |
|||
|
|||
To "propagate" a work means to do anything with it that, without |
|||
permission, would make you directly or secondarily liable for |
|||
infringement under applicable copyright law, except executing it on a |
|||
computer or modifying a private copy. Propagation includes copying, |
|||
distribution (with or without modification), making available to the |
|||
public, and in some countries other activities as well. |
|||
|
|||
To "convey" a work means any kind of propagation that enables other |
|||
parties to make or receive copies. Mere interaction with a user through |
|||
a computer network, with no transfer of a copy, is not conveying. |
|||
|
|||
An interactive user interface displays "Appropriate Legal Notices" |
|||
to the extent that it includes a convenient and prominently visible |
|||
feature that (1) displays an appropriate copyright notice, and (2) |
|||
tells the user that there is no warranty for the work (except to the |
|||
extent that warranties are provided), that licensees may convey the |
|||
work under this License, and how to view a copy of this License. If |
|||
the interface presents a list of user commands or options, such as a |
|||
menu, a prominent item in the list meets this criterion. |
|||
|
|||
1. Source Code. |
|||
|
|||
The "source code" for a work means the preferred form of the work |
|||
for making modifications to it. "Object code" means any non-source |
|||
form of a work. |
|||
|
|||
A "Standard Interface" means an interface that either is an official |
|||
standard defined by a recognized standards body, or, in the case of |
|||
interfaces specified for a particular programming language, one that |
|||
is widely used among developers working in that language. |
|||
|
|||
The "System Libraries" of an executable work include anything, other |
|||
than the work as a whole, that (a) is included in the normal form of |
|||
packaging a Major Component, but which is not part of that Major |
|||
Component, and (b) serves only to enable use of the work with that |
|||
Major Component, or to implement a Standard Interface for which an |
|||
implementation is available to the public in source code form. A |
|||
"Major Component", in this context, means a major essential component |
|||
(kernel, window system, and so on) of the specific operating system |
|||
(if any) on which the executable work runs, or a compiler used to |
|||
produce the work, or an object code interpreter used to run it. |
|||
|
|||
The "Corresponding Source" for a work in object code form means all |
|||
the source code needed to generate, install, and (for an executable |
|||
work) run the object code and to modify the work, including scripts to |
|||
control those activities. However, it does not include the work's |
|||
System Libraries, or general-purpose tools or generally available free |
|||
programs which are used unmodified in performing those activities but |
|||
which are not part of the work. For example, Corresponding Source |
|||
includes interface definition files associated with source files for |
|||
the work, and the source code for shared libraries and dynamically |
|||
linked subprograms that the work is specifically designed to require, |
|||
such as by intimate data communication or control flow between those |
|||
subprograms and other parts of the work. |
|||
|
|||
The Corresponding Source need not include anything that users |
|||
can regenerate automatically from other parts of the Corresponding |
|||
Source. |
|||
|
|||
The Corresponding Source for a work in source code form is that |
|||
same work. |
|||
|
|||
2. Basic Permissions. |
|||
|
|||
All rights granted under this License are granted for the term of |
|||
copyright on the Program, and are irrevocable provided the stated |
|||
conditions are met. This License explicitly affirms your unlimited |
|||
permission to run the unmodified Program. The output from running a |
|||
covered work is covered by this License only if the output, given its |
|||
content, constitutes a covered work. This License acknowledges your |
|||
rights of fair use or other equivalent, as provided by copyright law. |
|||
|
|||
You may make, run and propagate covered works that you do not |
|||
convey, without conditions so long as your license otherwise remains |
|||
in force. You may convey covered works to others for the sole purpose |
|||
of having them make modifications exclusively for you, or provide you |
|||
with facilities for running those works, provided that you comply with |
|||
the terms of this License in conveying all material for which you do |
|||
not control copyright. Those thus making or running the covered works |
|||
for you must do so exclusively on your behalf, under your direction |
|||
and control, on terms that prohibit them from making any copies of |
|||
your copyrighted material outside their relationship with you. |
|||
|
|||
Conveying under any other circumstances is permitted solely under |
|||
the conditions stated below. Sublicensing is not allowed; section 10 |
|||
makes it unnecessary. |
|||
|
|||
3. Protecting Users' Legal Rights From Anti-Circumvention Law. |
|||
|
|||
No covered work shall be deemed part of an effective technological |
|||
measure under any applicable law fulfilling obligations under article |
|||
11 of the WIPO copyright treaty adopted on 20 December 1996, or |
|||
similar laws prohibiting or restricting circumvention of such |
|||
measures. |
|||
|
|||
When you convey a covered work, you waive any legal power to forbid |
|||
circumvention of technological measures to the extent such circumvention |
|||
is effected by exercising rights under this License with respect to |
|||
the covered work, and you disclaim any intention to limit operation or |
|||
modification of the work as a means of enforcing, against the work's |
|||
users, your or third parties' legal rights to forbid circumvention of |
|||
technological measures. |
|||
|
|||
4. Conveying Verbatim Copies. |
|||
|
|||
You may convey verbatim copies of the Program's source code as you |
|||
receive it, in any medium, provided that you conspicuously and |
|||
appropriately publish on each copy an appropriate copyright notice; |
|||
keep intact all notices stating that this License and any |
|||
non-permissive terms added in accord with section 7 apply to the code; |
|||
keep intact all notices of the absence of any warranty; and give all |
|||
recipients a copy of this License along with the Program. |
|||
|
|||
You may charge any price or no price for each copy that you convey, |
|||
and you may offer support or warranty protection for a fee. |
|||
|
|||
5. Conveying Modified Source Versions. |
|||
|
|||
You may convey a work based on the Program, or the modifications to |
|||
produce it from the Program, in the form of source code under the |
|||
terms of section 4, provided that you also meet all of these conditions: |
|||
|
|||
a) The work must carry prominent notices stating that you modified |
|||
it, and giving a relevant date. |
|||
|
|||
b) The work must carry prominent notices stating that it is |
|||
released under this License and any conditions added under section |
|||
7. This requirement modifies the requirement in section 4 to |
|||
"keep intact all notices". |
|||
|
|||
c) You must license the entire work, as a whole, under this |
|||
License to anyone who comes into possession of a copy. This |
|||
License will therefore apply, along with any applicable section 7 |
|||
additional terms, to the whole of the work, and all its parts, |
|||
regardless of how they are packaged. This License gives no |
|||
permission to license the work in any other way, but it does not |
|||
invalidate such permission if you have separately received it. |
|||
|
|||
d) If the work has interactive user interfaces, each must display |
|||
Appropriate Legal Notices; however, if the Program has interactive |
|||
interfaces that do not display Appropriate Legal Notices, your |
|||
work need not make them do so. |
|||
|
|||
A compilation of a covered work with other separate and independent |
|||
works, which are not by their nature extensions of the covered work, |
|||
and which are not combined with it such as to form a larger program, |
|||
in or on a volume of a storage or distribution medium, is called an |
|||
"aggregate" if the compilation and its resulting copyright are not |
|||
used to limit the access or legal rights of the compilation's users |
|||
beyond what the individual works permit. Inclusion of a covered work |
|||
in an aggregate does not cause this License to apply to the other |
|||
parts of the aggregate. |
|||
|
|||
6. Conveying Non-Source Forms. |
|||
|
|||
You may convey a covered work in object code form under the terms |
|||
of sections 4 and 5, provided that you also convey the |
|||
machine-readable Corresponding Source under the terms of this License, |
|||
in one of these ways: |
|||
|
|||
a) Convey the object code in, or embodied in, a physical product |
|||
(including a physical distribution medium), accompanied by the |
|||
Corresponding Source fixed on a durable physical medium |
|||
customarily used for software interchange. |
|||
|
|||
b) Convey the object code in, or embodied in, a physical product |
|||
(including a physical distribution medium), accompanied by a |
|||
written offer, valid for at least three years and valid for as |
|||
long as you offer spare parts or customer support for that product |
|||
model, to give anyone who possesses the object code either (1) a |
|||
copy of the Corresponding Source for all the software in the |
|||
product that is covered by this License, on a durable physical |
|||
medium customarily used for software interchange, for a price no |
|||
more than your reasonable cost of physically performing this |
|||
conveying of source, or (2) access to copy the |
|||
Corresponding Source from a network server at no charge. |
|||
|
|||
c) Convey individual copies of the object code with a copy of the |
|||
written offer to provide the Corresponding Source. This |
|||
alternative is allowed only occasionally and noncommercially, and |
|||
only if you received the object code with such an offer, in accord |
|||
with subsection 6b. |
|||
|
|||
d) Convey the object code by offering access from a designated |
|||
place (gratis or for a charge), and offer equivalent access to the |
|||
Corresponding Source in the same way through the same place at no |
|||
further charge. You need not require recipients to copy the |
|||
Corresponding Source along with the object code. If the place to |
|||
copy the object code is a network server, the Corresponding Source |
|||
may be on a different server (operated by you or a third party) |
|||
that supports equivalent copying facilities, provided you maintain |
|||
clear directions next to the object code saying where to find the |
|||
Corresponding Source. Regardless of what server hosts the |
|||
Corresponding Source, you remain obligated to ensure that it is |
|||
available for as long as needed to satisfy these requirements. |
|||
|
|||
e) Convey the object code using peer-to-peer transmission, provided |
|||
you inform other peers where the object code and Corresponding |
|||
Source of the work are being offered to the general public at no |
|||
charge under subsection 6d. |
|||
|
|||
A separable portion of the object code, whose source code is excluded |
|||
from the Corresponding Source as a System Library, need not be |
|||
included in conveying the object code work. |
|||
|
|||
A "User Product" is either (1) a "consumer product", which means any |
|||
tangible personal property which is normally used for personal, family, |
|||
or household purposes, or (2) anything designed or sold for incorporation |
|||
into a dwelling. In determining whether a product is a consumer product, |
|||
doubtful cases shall be resolved in favor of coverage. For a particular |
|||
product received by a particular user, "normally used" refers to a |
|||
typical or common use of that class of product, regardless of the status |
|||
of the particular user or of the way in which the particular user |
|||
actually uses, or expects or is expected to use, the product. A product |
|||
is a consumer product regardless of whether the product has substantial |
|||
commercial, industrial or non-consumer uses, unless such uses represent |
|||
the only significant mode of use of the product. |
|||
|
|||
"Installation Information" for a User Product means any methods, |
|||
procedures, authorization keys, or other information required to install |
|||
and execute modified versions of a covered work in that User Product from |
|||
a modified version of its Corresponding Source. The information must |
|||
suffice to ensure that the continued functioning of the modified object |
|||
code is in no case prevented or interfered with solely because |
|||
modification has been made. |
|||
|
|||
If you convey an object code work under this section in, or with, or |
|||
specifically for use in, a User Product, and the conveying occurs as |
|||
part of a transaction in which the right of possession and use of the |
|||
User Product is transferred to the recipient in perpetuity or for a |
|||
fixed term (regardless of how the transaction is characterized), the |
|||
Corresponding Source conveyed under this section must be accompanied |
|||
by the Installation Information. But this requirement does not apply |
|||
if neither you nor any third party retains the ability to install |
|||
modified object code on the User Product (for example, the work has |
|||
been installed in ROM). |
|||
|
|||
The requirement to provide Installation Information does not include a |
|||
requirement to continue to provide support service, warranty, or updates |
|||
for a work that has been modified or installed by the recipient, or for |
|||
the User Product in which it has been modified or installed. Access to a |
|||
network may be denied when the modification itself materially and |
|||
adversely affects the operation of the network or violates the rules and |
|||
protocols for communication across the network. |
|||
|
|||
Corresponding Source conveyed, and Installation Information provided, |
|||
in accord with this section must be in a format that is publicly |
|||
documented (and with an implementation available to the public in |
|||
source code form), and must require no special password or key for |
|||
unpacking, reading or copying. |
|||
|
|||
7. Additional Terms. |
|||
|
|||
"Additional permissions" are terms that supplement the terms of this |
|||
License by making exceptions from one or more of its conditions. |
|||
Additional permissions that are applicable to the entire Program shall |
|||
be treated as though they were included in this License, to the extent |
|||
that they are valid under applicable law. If additional permissions |
|||
apply only to part of the Program, that part may be used separately |
|||
under those permissions, but the entire Program remains governed by |
|||
this License without regard to the additional permissions. |
|||
|
|||
When you convey a copy of a covered work, you may at your option |
|||
remove any additional permissions from that copy, or from any part of |
|||
it. (Additional permissions may be written to require their own |
|||
removal in certain cases when you modify the work.) You may place |
|||
additional permissions on material, added by you to a covered work, |
|||
for which you have or can give appropriate copyright permission. |
|||
|
|||
Notwithstanding any other provision of this License, for material you |
|||
add to a covered work, you may (if authorized by the copyright holders of |
|||
that material) supplement the terms of this License with terms: |
|||
|
|||
a) Disclaiming warranty or limiting liability differently from the |
|||
terms of sections 15 and 16 of this License; or |
|||
|
|||
b) Requiring preservation of specified reasonable legal notices or |
|||
author attributions in that material or in the Appropriate Legal |
|||
Notices displayed by works containing it; or |
|||
|
|||
c) Prohibiting misrepresentation of the origin of that material, or |
|||
requiring that modified versions of such material be marked in |
|||
reasonable ways as different from the original version; or |
|||
|
|||
d) Limiting the use for publicity purposes of names of licensors or |
|||
authors of the material; or |
|||
|
|||
e) Declining to grant rights under trademark law for use of some |
|||
trade names, trademarks, or service marks; or |
|||
|
|||
f) Requiring indemnification of licensors and authors of that |
|||
material by anyone who conveys the material (or modified versions of |
|||
it) with contractual assumptions of liability to the recipient, for |
|||
any liability that these contractual assumptions directly impose on |
|||
those licensors and authors. |
|||
|
|||
All other non-permissive additional terms are considered "further |
|||
restrictions" within the meaning of section 10. If the Program as you |
|||
received it, or any part of it, contains a notice stating that it is |
|||
governed by this License along with a term that is a further |
|||
restriction, you may remove that term. If a license document contains |
|||
a further restriction but permits relicensing or conveying under this |
|||
License, you may add to a covered work material governed by the terms |
|||
of that license document, provided that the further restriction does |
|||
not survive such relicensing or conveying. |
|||
|
|||
If you add terms to a covered work in accord with this section, you |
|||
must place, in the relevant source files, a statement of the |
|||
additional terms that apply to those files, or a notice indicating |
|||
where to find the applicable terms. |
|||
|
|||
Additional terms, permissive or non-permissive, may be stated in the |
|||
form of a separately written license, or stated as exceptions; |
|||
the above requirements apply either way. |
|||
|
|||
8. Termination. |
|||
|
|||
You may not propagate or modify a covered work except as expressly |
|||
provided under this License. Any attempt otherwise to propagate or |
|||
modify it is void, and will automatically terminate your rights under |
|||
this License (including any patent licenses granted under the third |
|||
paragraph of section 11). |
|||
|
|||
However, if you cease all violation of this License, then your |
|||
license from a particular copyright holder is reinstated (a) |
|||
provisionally, unless and until the copyright holder explicitly and |
|||
finally terminates your license, and (b) permanently, if the copyright |
|||
holder fails to notify you of the violation by some reasonable means |
|||
prior to 60 days after the cessation. |
|||
|
|||
Moreover, your license from a particular copyright holder is |
|||
reinstated permanently if the copyright holder notifies you of the |
|||
violation by some reasonable means, this is the first time you have |
|||
received notice of violation of this License (for any work) from that |
|||
copyright holder, and you cure the violation prior to 30 days after |
|||
your receipt of the notice. |
|||
|
|||
Termination of your rights under this section does not terminate the |
|||
licenses of parties who have received copies or rights from you under |
|||
this License. If your rights have been terminated and not permanently |
|||
reinstated, you do not qualify to receive new licenses for the same |
|||
material under section 10. |
|||
|
|||
9. Acceptance Not Required for Having Copies. |
|||
|
|||
You are not required to accept this License in order to receive or |
|||
run a copy of the Program. Ancillary propagation of a covered work |
|||
occurring solely as a consequence of using peer-to-peer transmission |
|||
to receive a copy likewise does not require acceptance. However, |
|||
nothing other than this License grants you permission to propagate or |
|||
modify any covered work. These actions infringe copyright if you do |
|||
not accept this License. Therefore, by modifying or propagating a |
|||
covered work, you indicate your acceptance of this License to do so. |
|||
|
|||
10. Automatic Licensing of Downstream Recipients. |
|||
|
|||
Each time you convey a covered work, the recipient automatically |
|||
receives a license from the original licensors, to run, modify and |
|||
propagate that work, subject to this License. You are not responsible |
|||
for enforcing compliance by third parties with this License. |
|||
|
|||
An "entity transaction" is a transaction transferring control of an |
|||
organization, or substantially all assets of one, or subdividing an |
|||
organization, or merging organizations. If propagation of a covered |
|||
work results from an entity transaction, each party to that |
|||
transaction who receives a copy of the work also receives whatever |
|||
licenses to the work the party's predecessor in interest had or could |
|||
give under the previous paragraph, plus a right to possession of the |
|||
Corresponding Source of the work from the predecessor in interest, if |
|||
the predecessor has it or can get it with reasonable efforts. |
|||
|
|||
You may not impose any further restrictions on the exercise of the |
|||
rights granted or affirmed under this License. For example, you may |
|||
not impose a license fee, royalty, or other charge for exercise of |
|||
rights granted under this License, and you may not initiate litigation |
|||
(including a cross-claim or counterclaim in a lawsuit) alleging that |
|||
any patent claim is infringed by making, using, selling, offering for |
|||
sale, or importing the Program or any portion of it. |
|||
|
|||
11. Patents. |
|||
|
|||
A "contributor" is a copyright holder who authorizes use under this |
|||
License of the Program or a work on which the Program is based. The |
|||
work thus licensed is called the contributor's "contributor version". |
|||
|
|||
A contributor's "essential patent claims" are all patent claims |
|||
owned or controlled by the contributor, whether already acquired or |
|||
hereafter acquired, that would be infringed by some manner, permitted |
|||
by this License, of making, using, or selling its contributor version, |
|||
but do not include claims that would be infringed only as a |
|||
consequence of further modification of the contributor version. For |
|||
purposes of this definition, "control" includes the right to grant |
|||
patent sublicenses in a manner consistent with the requirements of |
|||
this License. |
|||
|
|||
Each contributor grants you a non-exclusive, worldwide, royalty-free |
|||
patent license under the contributor's essential patent claims, to |
|||
make, use, sell, offer for sale, import and otherwise run, modify and |
|||
propagate the contents of its contributor version. |
|||
|
|||
In the following three paragraphs, a "patent license" is any express |
|||
agreement or commitment, however denominated, not to enforce a patent |
|||
(such as an express permission to practice a patent or covenant not to |
|||
sue for patent infringement). To "grant" such a patent license to a |
|||
party means to make such an agreement or commitment not to enforce a |
|||
patent against the party. |
|||
|
|||
If you convey a covered work, knowingly relying on a patent license, |
|||
and the Corresponding Source of the work is not available for anyone |
|||
to copy, free of charge and under the terms of this License, through a |
|||
publicly available network server or other readily accessible means, |
|||
then you must either (1) cause the Corresponding Source to be so |
|||
available, or (2) arrange to deprive yourself of the benefit of the |
|||
patent license for this particular work, or (3) arrange, in a manner |
|||
consistent with the requirements of this License, to extend the patent |
|||
license to downstream recipients. "Knowingly relying" means you have |
|||
actual knowledge that, but for the patent license, your conveying the |
|||
covered work in a country, or your recipient's use of the covered work |
|||
in a country, would infringe one or more identifiable patents in that |
|||
country that you have reason to believe are valid. |
|||
|
|||
If, pursuant to or in connection with a single transaction or |
|||
arrangement, you convey, or propagate by procuring conveyance of, a |
|||
covered work, and grant a patent license to some of the parties |
|||
receiving the covered work authorizing them to use, propagate, modify |
|||
or convey a specific copy of the covered work, then the patent license |
|||
you grant is automatically extended to all recipients of the covered |
|||
work and works based on it. |
|||
|
|||
A patent license is "discriminatory" if it does not include within |
|||
the scope of its coverage, prohibits the exercise of, or is |
|||
conditioned on the non-exercise of one or more of the rights that are |
|||
specifically granted under this License. You may not convey a covered |
|||
work if you are a party to an arrangement with a third party that is |
|||
in the business of distributing software, under which you make payment |
|||
to the third party based on the extent of your activity of conveying |
|||
the work, and under which the third party grants, to any of the |
|||
parties who would receive the covered work from you, a discriminatory |
|||
patent license (a) in connection with copies of the covered work |
|||
conveyed by you (or copies made from those copies), or (b) primarily |
|||
for and in connection with specific products or compilations that |
|||
contain the covered work, unless you entered into that arrangement, |
|||
or that patent license was granted, prior to 28 March 2007. |
|||
|
|||
Nothing in this License shall be construed as excluding or limiting |
|||
any implied license or other defenses to infringement that may |
|||
otherwise be available to you under applicable patent law. |
|||
|
|||
12. No Surrender of Others' Freedom. |
|||
|
|||
If conditions are imposed on you (whether by court order, agreement or |
|||
otherwise) that contradict the conditions of this License, they do not |
|||
excuse you from the conditions of this License. If you cannot convey a |
|||
covered work so as to satisfy simultaneously your obligations under this |
|||
License and any other pertinent obligations, then as a consequence you may |
|||
not convey it at all. For example, if you agree to terms that obligate you |
|||
to collect a royalty for further conveying from those to whom you convey |
|||
the Program, the only way you could satisfy both those terms and this |
|||
License would be to refrain entirely from conveying the Program. |
|||
|
|||
13. Use with the GNU Affero General Public License. |
|||
|
|||
Notwithstanding any other provision of this License, you have |
|||
permission to link or combine any covered work with a work licensed |
|||
under version 3 of the GNU Affero General Public License into a single |
|||
combined work, and to convey the resulting work. The terms of this |
|||
License will continue to apply to the part which is the covered work, |
|||
but the special requirements of the GNU Affero General Public License, |
|||
section 13, concerning interaction through a network will apply to the |
|||
combination as such. |
|||
|
|||
14. Revised Versions of this License. |
|||
|
|||
The Free Software Foundation may publish revised and/or new versions of |
|||
the GNU General Public License from time to time. Such new versions will |
|||
be similar in spirit to the present version, but may differ in detail to |
|||
address new problems or concerns. |
|||
|
|||
Each version is given a distinguishing version number. If the |
|||
Program specifies that a certain numbered version of the GNU General |
|||
Public License "or any later version" applies to it, you have the |
|||
option of following the terms and conditions either of that numbered |
|||
version or of any later version published by the Free Software |
|||
Foundation. If the Program does not specify a version number of the |
|||
GNU General Public License, you may choose any version ever published |
|||
by the Free Software Foundation. |
|||
|
|||
If the Program specifies that a proxy can decide which future |
|||
versions of the GNU General Public License can be used, that proxy's |
|||
public statement of acceptance of a version permanently authorizes you |
|||
to choose that version for the Program. |
|||
|
|||
Later license versions may give you additional or different |
|||
permissions. However, no additional obligations are imposed on any |
|||
author or copyright holder as a result of your choosing to follow a |
|||
later version. |
|||
|
|||
15. Disclaimer of Warranty. |
|||
|
|||
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY |
|||
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT |
|||
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY |
|||
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, |
|||
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR |
|||
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM |
|||
IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF |
|||
ALL NECESSARY SERVICING, REPAIR OR CORRECTION. |
|||
|
|||
16. Limitation of Liability. |
|||
|
|||
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING |
|||
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS |
|||
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY |
|||
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE |
|||
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF |
|||
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD |
|||
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), |
|||
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF |
|||
SUCH DAMAGES. |
|||
|
|||
17. Interpretation of Sections 15 and 16. |
|||
|
|||
If the disclaimer of warranty and limitation of liability provided |
|||
above cannot be given local legal effect according to their terms, |
|||
reviewing courts shall apply local law that most closely approximates |
|||
an absolute waiver of all civil liability in connection with the |
|||
Program, unless a warranty or assumption of liability accompanies a |
|||
copy of the Program in return for a fee. |
|||
|
|||
END OF TERMS AND CONDITIONS |
|||
|
|||
How to Apply These Terms to Your New Programs |
|||
|
|||
If you develop a new program, and you want it to be of the greatest |
|||
possible use to the public, the best way to achieve this is to make it |
|||
free software which everyone can redistribute and change under these terms. |
|||
|
|||
To do so, attach the following notices to the program. It is safest |
|||
to attach them to the start of each source file to most effectively |
|||
state the exclusion of warranty; and each file should have at least |
|||
the "copyright" line and a pointer to where the full notice is found. |
|||
|
|||
{one line to give the program's name and a brief idea of what it does.} |
|||
Copyright (C) {year} {name of author} |
|||
|
|||
This program is free software: you can redistribute it and/or modify |
|||
it under the terms of the GNU General Public License as published by |
|||
the Free Software Foundation, either version 3 of the License, or |
|||
(at your option) any later version. |
|||
|
|||
This program is distributed in the hope that it will be useful, |
|||
but WITHOUT ANY WARRANTY; without even the implied warranty of |
|||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
|||
GNU General Public License for more details. |
|||
|
|||
You should have received a copy of the GNU General Public License |
|||
along with this program. If not, see <http://www.gnu.org/licenses/>. |
|||
|
|||
Also add information on how to contact you by electronic and paper mail. |
|||
|
|||
If the program does terminal interaction, make it output a short |
|||
notice like this when it starts in an interactive mode: |
|||
|
|||
{project} Copyright (C) {year} {fullname} |
|||
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. |
|||
This is free software, and you are welcome to redistribute it |
|||
under certain conditions; type `show c' for details. |
|||
|
|||
The hypothetical commands `show w' and `show c' should show the appropriate |
|||
parts of the General Public License. Of course, your program's commands |
|||
might be different; for a GUI interface, you would use an "about box". |
|||
|
|||
You should also get your employer (if you work as a programmer) or school, |
|||
if any, to sign a "copyright disclaimer" for the program, if necessary. |
|||
For more information on this, and how to apply and follow the GNU GPL, see |
|||
<http://www.gnu.org/licenses/>. |
|||
|
|||
The GNU General Public License does not permit incorporating your program |
|||
into proprietary programs. If your program is a subroutine library, you |
|||
may consider it more useful to permit linking proprietary applications with |
|||
the library. If this is what you want to do, use the GNU Lesser General |
|||
Public License instead of this License. But first, please read |
|||
<http://www.gnu.org/philosophy/why-not-lgpl.html>. |
@ -0,0 +1,15 @@ |
|||
.PHONY: clean pkg deps run |
|||
|
|||
pkg: |
|||
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home mvn --quiet package |
|||
cp target/jLZJD-1.0-SNAPSHOT.jar ../../inst/java |
|||
cp deps/*jar ../../inst/java |
|||
|
|||
clean: |
|||
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home mvn clean |
|||
|
|||
deps: |
|||
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home mvn dependency:copy-dependencies -DoutputDirectory=deps |
|||
|
|||
new: |
|||
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home mvn archetype:generate -DgroupId=com.edwardraff.jLZJD -DartifactId=jLZJD -DarchetypeArtifactId=maven-archetype-quickstart -DinteractiveMode=false |
@ -0,0 +1,59 @@ |
|||
# jLZJD |
|||
|
|||
jLZJD is a Java implementatio of the *Lempel-Ziv Jaccard Distance*, a distance metric designed for arbitrary byte sequences, and originally used for malware classification. It was inspired by and developed as an alternative to the [Normalized Compression Distance](https://en.wikipedia.org/wiki/Normalized_compression_distance). But, we've also found it useful for similarity digest taks, where one would normaly use either [ssdeep](http://www.forensicswiki.org/wiki/Ssdeep) or [sdhash](http://roussev.net/sdhash/tutorial/03-quick.html). |
|||
|
|||
For this reason, this code base not only implements the LJZD algorithm, but also provides an comand line interface that mimics the comands of sdhash, so you can easily try it on new data / as a almost drop in replacement in your existing workflow. |
|||
|
|||
Below are the comandline options that jLZJD currently implements from sdhash |
|||
``` |
|||
-r [ --deep ] generate SDBFs from directories and files |
|||
-c [ --compare ] compare SDBFs in file, or two SDBF files |
|||
-g [ --gen-compare ] compare all pairs in source data |
|||
-t [ --threshold ] arg (=20) only show results >=threshold |
|||
-p [ --threads ] arg restrict compute threads to N threads |
|||
-o [ --output ] arg send output to files |
|||
``` |
|||
|
|||
|
|||
## Why use jLZJD? |
|||
|
|||
If you need to find similar byte sequences, and your byte sequences can be long (>500kb), then you should consuder using LZJD and this implementation! LZJD is fast, efficient, and we've found it to be more accurate than the previously existing options. If you want to know more nity gritty details, check out the two papers listed under citations. |
|||
|
|||
There is also a [C++ version](https://github.com/EdwardRaff/LZJD) in the works, but its not as well done / complete yet. |
|||
|
|||
## Citations |
|||
|
|||
There are currently two papers related to LZJD. The [original paper](http://www.edwardraff.com/publications/alternative-ncd-lzjd.pdf) that introduces it, and a [followup paper](https://arxiv.org/abs/1708.03346) that shows how LZJD can be used inplace of ssdeep and sdhash. Please cite the first paper if you use LZJD at all, and please cite the second as well if you use this implementation! |
|||
|
|||
``` |
|||
@inproceedings{raff_lzjd_2017, |
|||
author = {Raff, Edward and Nicholas, Charles}, |
|||
title = {An Alternative to NCD for Large Sequences, Lempel-Ziv Jaccard Distance}, |
|||
booktitle = {Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining}, |
|||
series = {KDD '17}, |
|||
year = {2017}, |
|||
isbn = {978-1-4503-4887-4}, |
|||
location = {Halifax, NS, Canada}, |
|||
pages = {1007--1015}, |
|||
numpages = {9}, |
|||
url = {http://doi.acm.org/10.1145/3097983.3098111}, |
|||
doi = {10.1145/3097983.3098111}, |
|||
acmid = {3098111}, |
|||
publisher = {ACM}, |
|||
address = {New York, NY, USA}, |
|||
keywords = {cyber security, jaccard similarity, lempel-ziv, malware classification, normalized compression distance}, |
|||
} |
|||
|
|||
@article{raff_lzjd_digest, |
|||
archivePrefix = {arXiv}, |
|||
arxivId = {1708.03346}, |
|||
author = {Raff, Edward and Nicholas, Charles K.}, |
|||
eprint = {1708.03346}, |
|||
institution = {University of Maryland, Baltimore County}, |
|||
journal = {arXiv preprint arXiv:1708.03346}, |
|||
month = {aug}, |
|||
title = {{Lempel-Ziv Jaccard Distance, an Effective Alternative to Ssdeep and Sdhash}}, |
|||
url = {https://arxiv.org/abs/1708.03346}, |
|||
year = {2017} |
|||
} |
|||
``` |
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@ -0,0 +1,70 @@ |
|||
<?xml version="1.0" encoding="UTF-8"?> |
|||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> |
|||
<modelVersion>4.0.0</modelVersion> |
|||
<groupId>com.edwardraff</groupId> |
|||
<artifactId>jLZJD</artifactId> |
|||
<version>1.0-SNAPSHOT</version> |
|||
<packaging>jar</packaging> |
|||
<properties> |
|||
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> |
|||
<maven.compiler.source>1.8</maven.compiler.source> |
|||
<maven.compiler.target>1.8</maven.compiler.target> |
|||
</properties> |
|||
<dependencies> |
|||
<dependency> |
|||
<groupId>com.edwardraff</groupId> |
|||
<artifactId>JSAT</artifactId> |
|||
<version>0.0.8</version> |
|||
</dependency> |
|||
<dependency> |
|||
<groupId>junit</groupId> |
|||
<artifactId>junit</artifactId> |
|||
<version>4.12</version> |
|||
<scope>test</scope> |
|||
</dependency> |
|||
<dependency> |
|||
<groupId>org.hamcrest</groupId> |
|||
<artifactId>hamcrest-core</artifactId> |
|||
<version>1.3</version> |
|||
<scope>test</scope> |
|||
</dependency> |
|||
<dependency> |
|||
<groupId>com.beust</groupId> |
|||
<artifactId>jcommander</artifactId> |
|||
<version>1.60</version> |
|||
</dependency> |
|||
<dependency> |
|||
<groupId>com.google.guava</groupId> |
|||
<artifactId>guava</artifactId> |
|||
<version>21.0</version> |
|||
</dependency> |
|||
</dependencies> |
|||
<build> |
|||
<plugins> |
|||
<plugin> |
|||
<artifactId>maven-assembly-plugin</artifactId> |
|||
<configuration> |
|||
<archive> |
|||
<manifest> |
|||
<mainClass> |
|||
com.edwardraff.jlzjd.Main |
|||
</mainClass> |
|||
</manifest> |
|||
</archive> |
|||
<descriptorRefs> |
|||
<descriptorRef>jar-with-dependencies</descriptorRef> |
|||
</descriptorRefs> |
|||
</configuration> |
|||
<executions> |
|||
<execution> |
|||
<id>make-assembly</id> <!-- this is used for inheritance merges --> |
|||
<phase>package</phase> <!-- bind to the packaging phase --> |
|||
<goals> |
|||
<goal>single</goal> |
|||
</goals> |
|||
</execution> |
|||
</executions> |
|||
</plugin> |
|||
</plugins> |
|||
</build> |
|||
</project> |
@ -0,0 +1,260 @@ |
|||
|
|||
package com.edwardraff.jlzjd; |
|||
|
|||
import java.io.Serializable; |
|||
import java.util.*; |
|||
import static jsat.utils.ClosedHashingUtil.*; |
|||
|
|||
/** |
|||
* A utility class for efficiently storing a set of integers. The implementation |
|||
* is based on Algorithm D (Open addressing with double hashing) from Knuth's |
|||
* TAOCP page 528. |
|||
* |
|||
* @author Edward Raff |
|||
*/ |
|||
public class IntSetNoRemove extends AbstractSet<Integer> implements Serializable |
|||
{ |
|||
|
|||
private static final long serialVersionUID = -2175363824037596497L; |
|||
|
|||
private static final int DEFAULT_CAPACITY = 8; |
|||
|
|||
private float loadFactor; |
|||
|
|||
private int used = 0; |
|||
/** |
|||
* true if occupied, false otherwise (i.e., free) |
|||
*/ |
|||
private boolean[] status; |
|||
private int[] keys; |
|||
private final static boolean FREE = false; |
|||
private final static boolean OCCUPIED = true; |
|||
|
|||
/** |
|||
* Creates a new empty integer set |
|||
*/ |
|||
public IntSetNoRemove() |
|||
{ |
|||
this(DEFAULT_CAPACITY); |
|||
} |
|||
|
|||
/** |
|||
* Creates an empty integer set pre-allocated to store a specific number of |
|||
* items |
|||
* |
|||
* @param capacity the number of items to store |
|||
*/ |
|||
public IntSetNoRemove(int capacity) |
|||
{ |
|||
this(capacity, 0.75f); |
|||
} |
|||
|
|||
/** |
|||
* Creates an empty integer set pre-allocated to store a specific number of |
|||
* items |
|||
* |
|||
* @param capacity the number of items to store |
|||
* @param loadFactor the maximum ratio of used to un-used storage |
|||
*/ |
|||
public IntSetNoRemove(int capacity, float loadFactor) |
|||
{ |
|||
this.loadFactor = loadFactor; |
|||
int size = getNextPow2TwinPrime((int) Math.max(capacity / loadFactor, 4)); |
|||
status = new boolean[size]; |
|||
keys = new int[size]; |
|||
used = 0; |
|||
} |
|||
|
|||
/** |
|||
* Creates a new set of integers from the given set |
|||
* @param set the set of integers to create a copy of |
|||
*/ |
|||
public IntSetNoRemove(Set<Integer> set) |
|||
{ |
|||
this(set.size()); |
|||
for(Integer integer : set) |
|||
this.add(integer); |
|||
} |
|||
|
|||
/** |
|||
* Creates a set of integers from the given collection |
|||
* @param collection a collection of integers to create a set from |
|||
*/ |
|||
public IntSetNoRemove(Collection<Integer> collection) |
|||
{ |
|||
this(); |
|||
for(Integer integer : collection) |
|||
this.add(integer); |
|||
} |
|||
|
|||
|
|||
/** |
|||
* Gets the index of the given key. Based on that {@link #status} variable, |
|||
* the index is either the location to insert OR the location of the key. |
|||
* |
|||
* This method returns 2 integer table in the long. The lower 32 bits are |
|||
* the index that either contains the key, or is the first empty index. |
|||
* |
|||
* The upper 32 bits is the index of the first position marked as |
|||
* {@link #DELETED} either {@link Integer#MIN_VALUE} if no position was |
|||
* marked as DELETED while searching. |
|||
* |
|||
* @param key they key to search for |
|||
* @return the mixed long containing the index of the first DELETED position |
|||
* and the position that the key is in or the first EMPTY position found |
|||
*/ |
|||
private int getIndex(int key) |
|||
{ |
|||
//D1
|
|||
final int hash = key & 0x7fffffff; |
|||
int i = hash % keys.length; |
|||
|
|||
//D2
|
|||
if(status[i] == FREE || keys[i] == key) |
|||
return i; |
|||
|
|||
//D3
|
|||
final int c = 1 + (hash % (keys.length -2)); |
|||
|
|||
while(true)//this loop will terminate
|
|||
{ |
|||
//D4
|
|||
i -= c; |
|||
if(i < 0) |
|||
i += keys.length; |
|||
//D5
|
|||
if( status[i] == FREE || keys[i] == key) |
|||
return i; |
|||
} |
|||
} |
|||
|
|||
private void enlargeIfNeeded() |
|||
{ |
|||
if(used < keys.length*loadFactor) |
|||
return; |
|||
//enlarge
|
|||
final boolean[] oldSatus = status; |
|||
final int[] oldKeys = keys; |
|||
|
|||
int newSize = getNextPow2TwinPrime(status.length*3/2);//it will actually end up doubling in size since we have twin primes spaced that was
|
|||
status = new boolean[newSize]; |
|||
keys = new int[newSize]; |
|||
|
|||
used = 0; |
|||
for(int oldIndex = 0; oldIndex < oldSatus.length; oldIndex++) |
|||
if(oldSatus[oldIndex] == OCCUPIED) |
|||
add(oldKeys[oldIndex]); |
|||
} |
|||
|
|||
@Override |
|||
public void clear() |
|||
{ |
|||
used = 0; |
|||
Arrays.fill(status, FREE); |
|||
} |
|||
|
|||
@Override |
|||
public boolean add(Integer e) |
|||
{ |
|||
if(e == null) |
|||
return false; |
|||
return add(e.intValue()); |
|||
} |
|||
|
|||
/** |
|||
* |
|||
* @param e element to be added to this set |
|||
* @return true if this set did not already contain the specified element |
|||
*/ |
|||
public boolean add(int e) |
|||
{ |
|||
final int key = e; |
|||
int pair_index = getIndex(key); |
|||
// int deletedIndex = (int) (pair_index >>> 32);
|
|||
// int valOrFreeIndex = (int) (pair_index & INT_MASK);
|
|||
int valOrFreeIndex = pair_index; |
|||
|
|||
if(status[valOrFreeIndex] == OCCUPIED)//easy case
|
|||
{ |
|||
return false;//we already had this item in the set!
|
|||
} |
|||
//else, not present
|
|||
int i = valOrFreeIndex; |
|||
// if(deletedIndex >= 0)//use occupied spot instead
|
|||
// i = deletedIndex;
|
|||
|
|||
status[i] = OCCUPIED; |
|||
keys[i] = key; |
|||
used++; |
|||
|
|||
enlargeIfNeeded(); |
|||
|
|||
return true;//item was not in the set previously
|
|||
} |
|||
|
|||
public boolean contains(int o) |
|||
{ |
|||
int index = getIndex(o); |
|||
return status[index] == OCCUPIED;//would be FREE if we didn't have the key
|
|||
} |
|||
|
|||
|
|||
@Override |
|||
public boolean contains(Object o) |
|||
{ |
|||
if(o != null && o instanceof Integer) |
|||
return contains(((Integer)o).intValue()); |
|||
else |
|||
return false; |
|||
} |
|||
|
|||
|
|||
@Override |
|||
public Iterator<Integer> iterator() |
|||
{ |
|||
//find the first starting inded
|
|||
int START = 0; |
|||
while (START < status.length && status[START] != OCCUPIED) |
|||
START++; |
|||
if (START == status.length) |
|||
return Collections.emptyIterator(); |
|||
final int startPos = START; |
|||
|
|||
return new Iterator<Integer>() |
|||
{ |
|||
int pos = startPos; |
|||
int prevPos = -1; |
|||
|
|||
@Override |
|||
public boolean hasNext() |
|||
{ |
|||
return pos < status.length; |
|||
} |
|||
|
|||
@Override |
|||
public Integer next() |
|||
{ |
|||
//final int make so that object remains good after we call next again
|
|||
final int oldPos = prevPos = pos++; |
|||
//find next
|
|||
while (pos < status.length && status[pos] != OCCUPIED) |
|||
pos++; |
|||
//and return new object
|
|||
return keys[oldPos]; |
|||
} |
|||
|
|||
@Override |
|||
public void remove() |
|||
{ |
|||
throw new UnsupportedOperationException(); |
|||
} |
|||
}; |
|||
} |
|||
|
|||
@Override |
|||
public int size() |
|||
{ |
|||
return used; |
|||
} |
|||
|
|||
} |
@ -0,0 +1,386 @@ |
|||
package com.edwardraff.jlzjd; |
|||
|
|||
import com.google.common.collect.Ordering; |
|||
import java.io.File; |
|||
import java.io.FileInputStream; |
|||
import java.io.IOException; |
|||
import java.io.InputStream; |
|||
import java.nio.ByteBuffer; |
|||
import java.nio.IntBuffer; |
|||
import java.util.Arrays; |
|||
import java.util.Collections; |
|||
import java.util.HashSet; |
|||
import java.util.List; |
|||
import java.util.Base64; |
|||
import java.util.concurrent.ConcurrentHashMap; |
|||
import java.util.concurrent.ConcurrentMap; |
|||
import java.util.concurrent.ExecutorService; |
|||
import java.util.concurrent.atomic.AtomicInteger; |
|||
import java.util.logging.Level; |
|||
import java.util.logging.Logger; |
|||
import jsat.classifiers.DataPoint; |
|||
import jsat.distributions.kernels.KernelTrick; |
|||
import jsat.linear.DenseVector; |
|||
import jsat.linear.Vec; |
|||
import jsat.linear.distancemetrics.DistanceMetric; |
|||
import jsat.parameters.Parameter; |
|||
import jsat.utils.IntList; |
|||
|
|||
/** |
|||
* |
|||
* @author Edward Raff |
|||
*/ |
|||
public class LZJDf implements DistanceMetric, KernelTrick |
|||
{ |
|||
static final ConcurrentMap<File, Integer> files = new ConcurrentHashMap<>(); |
|||
static final AtomicInteger file_counter = new AtomicInteger(); |
|||
static final ConcurrentMap<Integer, int[]> min_hashes = new ConcurrentHashMap<>(); |
|||
static ThreadLocal<HashSet<ByteBuffer>> localSets = ThreadLocal.withInitial(() -> new HashSet<>()); |
|||
static ThreadLocal<byte[]> localByteBuffer = ThreadLocal.withInitial(() -> new byte[4*1024]); |
|||
public static int min_hash_size = 1024; |
|||
|
|||
static final ThreadLocal<IntList> LOCAL_INT_LIST = ThreadLocal.withInitial(()->new IntList()); |
|||
static final ThreadLocal<IntSetNoRemove> LOCAL_X_SET = ThreadLocal.withInitial(()->new IntSetNoRemove(1024, 0.65f)); |
|||
|
|||
public static Integer minhashSize = 1024; |
|||
|
|||
/** |
|||
* Fills a set of ByteBuffers according the the LZ algorithm. Returns the |
|||
* set as a list of unique integer hashes found. |
|||
* |
|||
* @param ints the location t store all of the integer hashes of the sub-sequences |
|||
* @param is the byte source to hash |
|||
*/ |
|||
private static void getAllHashes(IntList ints, InputStream is) throws IOException |
|||
{ |
|||
IntSetNoRemove x_set = LOCAL_X_SET.get(); |
|||
x_set.clear(); |
|||
MurmurHash3 running_hash = new MurmurHash3(); |
|||
int pos = 0; |
|||
int end = 0; |
|||
byte[] buffer = localByteBuffer.get(); |
|||
|
|||
while(true) |
|||
{ |
|||
if(end == pos)//we need more bytes!
|
|||
{ |
|||
end = is.read(buffer); |
|||
if(end < 0) |
|||
break;//EOF, we are done
|
|||
pos = 0; |
|||
} |
|||
//else, procceed
|
|||
int hash = running_hash.pushByte(buffer[pos++]); |
|||
if(x_set.add(hash)) |
|||
{//never seen it before, put it in!
|
|||
ints.add(hash); |
|||
running_hash.reset(); |
|||
} |
|||
} |
|||
} |
|||
|
|||
/** |
|||
* Obtains a min-hash set for the given input file |
|||
* @param indx the unique index assigned for this file |
|||
* @param x_file the file to get the LZJDf min-hash of |
|||
* @param min_hash_size the max size for the min-hash |
|||
* @return an int array of the min-hash values in sorted order |
|||
* @throws IOException |
|||
*/ |
|||
protected static int[] getMinHash(int indx, File x_file, int min_hash_size) throws IOException |
|||
{ |
|||
int[] x_minset = min_hashes.get(indx); |
|||
if(x_minset == null) |
|||
{ |
|||
try(FileInputStream fis = new FileInputStream(x_file)) |
|||
{ |
|||
IntList hashes = LOCAL_INT_LIST.get(); |
|||
hashes.clear(); |
|||
getAllHashes(hashes, fis); |
|||
|
|||
List<Integer> sub_hashes = Ordering.natural().leastOf(hashes, Math.min(min_hash_size, hashes.size())); |
|||
|
|||
x_minset = new int[sub_hashes.size()]; |
|||
for(int i = 0; i < x_minset.length; i++) |
|||
x_minset[i] = sub_hashes.get(i); |
|||
Arrays.sort(x_minset); |
|||
|
|||
min_hashes.putIfAbsent(indx, x_minset); |
|||
} |
|||
} |
|||
|
|||
return x_minset; |
|||
} |
|||
|
|||
/** |
|||
* Obtains a DataPoint object for the given file, which stores a representation that can be used with this distance metric |
|||
* @param f the file to get a min-hash for |
|||
* @return a DataPoint that will correspond to the given file |
|||
*/ |
|||
public static DataPoint getDPforFile(File f) |
|||
{ |
|||
int id; |
|||
|
|||
id = file_counter.getAndIncrement(); |
|||
files.put(f, id); |
|||
|
|||
DenseVector dv = new DenseVector(1); |
|||
dv.set(0, id); |
|||
|
|||
try |
|||
{ |
|||
getMinHash(id, f, min_hash_size); |
|||
} |
|||
catch (IOException ex) |
|||
{ |
|||
Logger.getLogger(LZJDf.class.getName()).log(Level.SEVERE, null, ex); |
|||
} |
|||
|
|||
|
|||
return new DataPoint(dv); |
|||
} |
|||
|
|||
/** |
|||
* Obtains a DataPoint object for the given file, which stores a representation that can be used with this distance metric |
|||
* @param f the file to get a min-hash for |
|||
* @return a DataPoint that will correspond to the given file |
|||
*/ |
|||
public static int[] getMHforFile(File f) |
|||
{ |
|||
int id; |
|||
|
|||
id = file_counter.getAndIncrement(); |
|||
files.put(f, id); |
|||
|
|||
DenseVector dv = new DenseVector(1); |
|||
dv.set(0, id); |
|||
|
|||
try |
|||
{ |
|||
return getMinHash(id, f, min_hash_size); |
|||
} |
|||
catch (IOException ex) |
|||
{ |
|||
Logger.getLogger(LZJDf.class.getName()).log(Level.SEVERE, null, ex); |
|||
} |
|||
return new int[0]; |
|||
} |
|||
|
|||
|
|||
public static String toBase64(int[] hash) { |
|||
|
|||
ThreadLocal<byte[]> localTmpSpace = ThreadLocal.withInitial(()->new byte[minhashSize*Integer.BYTES]); |
|||
|
|||
try { |
|||
byte[] byte_tmp_space = localTmpSpace.get(); |
|||
ByteBuffer byteBuffer = ByteBuffer.wrap(byte_tmp_space); |
|||
IntBuffer intBuffer = byteBuffer.asIntBuffer(); |
|||
intBuffer.put(hash); |
|||
|
|||
String b64 = Base64.getEncoder().encodeToString(byte_tmp_space); |
|||
|
|||
return(b64); |
|||
|
|||
} catch (Exception e) { |
|||
return(""); |
|||
} |
|||
|
|||
} |
|||
|
|||
public static int[] fromBase64(String b64) { |
|||
|
|||
try { |
|||
|
|||
byte[] cmp = Base64.getDecoder().decode(b64); |
|||
int hashLen = cmp.length/Integer.BYTES; |
|||
int[] hash = new int[hashLen]; |
|||
IntBuffer readBack = ByteBuffer.wrap(cmp).asIntBuffer(); |
|||
for(int i = 0; i < hash.length; i++) hash[i] = readBack.get(i); |
|||
|
|||
return(hash); |
|||
|
|||
} catch (Exception e) { |
|||
|
|||
return(new int[0]); |
|||
|
|||
} |
|||
|
|||
} |
|||
|
|||
@Override |
|||
public boolean isSymmetric() |
|||
{ |
|||
return true; |
|||
} |
|||
|
|||
@Override |
|||
public boolean isSubadditive() |
|||
{ |
|||
return true; |
|||
} |
|||
|
|||
@Override |
|||
public boolean isIndiscemible() |
|||
{ |
|||
return true; |
|||
} |
|||
|
|||
@Override |
|||
public double metricBound() |
|||
{ |
|||
return 1; |
|||
} |
|||
|
|||
@Override |
|||
public boolean supportsAcceleration() |
|||
{ |
|||
return false; |
|||
} |
|||
|
|||
@Override |
|||
public List<Double> getAccelerationCache(List<? extends Vec> vecs) |
|||
{ |
|||
return null; |
|||
} |
|||
|
|||
@Override |
|||
public List<Double> getAccelerationCache(List<? extends Vec> vecs, ExecutorService threadpool) |
|||
{ |
|||
return null; |
|||
} |
|||
|
|||
|
|||
@Override |
|||
public double dist(Vec a, Vec b) |
|||
{ |
|||
int x = (int) a.get(0); |
|||
int y = (int) b.get(0); |
|||
|
|||
try |
|||
{ |
|||
int[] x_minset = getMinHash(x, null, min_hash_size); |
|||
int[] y_minset = getMinHash(y, null, min_hash_size); |
|||
|
|||
return dist(x_minset, y_minset); |
|||
|
|||
} |
|||
catch (IOException ex) |
|||
{ |
|||
Logger.getLogger(LZJDf.class.getName()).log(Level.SEVERE, null, ex); |
|||
} |
|||
|
|||
return 1; |
|||
} |
|||
|
|||
public static double dist(int[] x_minset, int[] y_minset) |
|||
{ |
|||
double sim = similarity(x_minset, y_minset); |
|||
return 1.0 - sim; |
|||
} |
|||
|
|||
public static double similarity(int[] x_minset, int[] y_minset) |
|||
{ |
|||
int same = 0; |
|||
int x_pos = 0, y_pos = 0; |
|||
while(x_pos < x_minset.length && y_pos < y_minset.length) |
|||
{ |
|||
int x_v = x_minset[x_pos]; |
|||
int y_v = y_minset[y_pos]; |
|||
if(x_v == y_v) |
|||
{ |
|||
same++; |
|||
x_pos++; |
|||
y_pos++; |
|||
} |
|||
else if(x_v < y_v) |
|||
x_pos++; |
|||
else |
|||
y_pos++; |
|||
} |
|||
double sim = same / (double) (x_minset.length + y_minset.length - same); |
|||
return sim; |
|||
} |
|||
|
|||
@Override |
|||
public double dist(int a, int b, List<? extends Vec> vecs, List<Double> cache) |
|||
{ |
|||
return dist(vecs.get(a), vecs.get(b)); |
|||
} |
|||
|
|||
@Override |
|||
public double dist(int a, Vec b, List<? extends Vec> vecs, List<Double> cache) |
|||
{ |
|||
return dist(vecs.get(a), b); |
|||
} |
|||
|
|||
@Override |
|||
public List<Double> getQueryInfo(Vec q) |
|||
{ |
|||
return null; |
|||
} |
|||
|
|||
@Override |
|||
public double dist(int a, Vec b, List<Double> qi, List<? extends Vec> vecs, List<Double> cache) |
|||
{ |
|||
return dist(vecs.get(a), b); |
|||
} |
|||
|
|||
@Override |
|||
public LZJDf clone() |
|||
{ |
|||
return this; |
|||
} |
|||
|
|||
@Override |
|||
public double eval(Vec a, Vec b) { |
|||
return 1-dist(a, b); |
|||
} |
|||
|
|||
@Override |
|||
public void addToCache(Vec newVec, List<Double> cache) { |
|||
|
|||
} |
|||
|
|||
@Override |
|||
public double eval(int a, Vec b, List<Double> qi, List<? extends Vec> vecs, List<Double> cache) { |
|||
return 1-dist(a, b, qi, vecs, cache); |
|||
} |
|||
|
|||
@Override |
|||
public double eval(int a, int b, List<? extends Vec> trainingSet, List<Double> cache) { |
|||
return 1-dist(a, b, trainingSet, cache); |
|||
} |
|||
|
|||
@Override |
|||
public double evalSum(List<? extends Vec> finalSet, List<Double> cache, double[] alpha, Vec y, int start, int end) { |
|||
double dot = 0; |
|||
for(int i = 0; i < alpha.length; i++) |
|||
if(alpha[i] != 0) |
|||
dot += alpha[i] * eval(i, y, null, finalSet, cache); |
|||
return dot; |
|||
} |
|||
|
|||
@Override |
|||
public double evalSum(List<? extends Vec> finalSet, List<Double> cache, double[] alpha, Vec y, List<Double> qi, int start, int end) { |
|||
double dot = 0; |
|||
for(int i = 0; i < alpha.length; i++) |
|||
if(alpha[i] != 0) |
|||
dot += alpha[i] * eval(i, y, qi, finalSet, cache); |
|||
return dot; |
|||
} |
|||
|
|||
@Override |
|||
public boolean normalized() { |
|||
return true; |
|||
} |
|||
|
|||
@Override |
|||
public List<Parameter> getParameters() { |
|||
return Collections.EMPTY_LIST; |
|||
} |
|||
|
|||
@Override |
|||
public Parameter getParameter(String paramName) { |
|||
return null; |
|||
} |
|||
} |
@ -0,0 +1,340 @@ |
|||
package com.edwardraff.jlzjd; |
|||
|
|||
import com.beust.jcommander.JCommander; |
|||
import com.beust.jcommander.Parameter; |
|||
import com.beust.jcommander.converters.FileConverter; |
|||
import java.io.*; |
|||
import java.nio.ByteBuffer; |
|||
import java.nio.IntBuffer; |
|||
import java.nio.file.Files; |
|||
import java.util.*; |
|||
import java.util.concurrent.ConcurrentLinkedQueue; |
|||
import java.util.concurrent.CountDownLatch; |
|||
import java.util.concurrent.ExecutorService; |
|||
import java.util.concurrent.Executors; |
|||
import java.util.concurrent.locks.ReentrantLock; |
|||
import java.util.logging.Level; |
|||
import java.util.logging.Logger; |
|||
import java.util.stream.IntStream; |
|||
import jsat.utils.SystemInfo; |
|||
|
|||
|
|||
/** |
|||
* |
|||
* @author Edward Raff <Raff.Edward@gmail.com> |
|||
*/ |
|||
public class Main |
|||
{ |
|||
@Parameter(names = { "-t", "--threshold" }, description = "only show results >=threshold") |
|||
public Integer threshold = 20; |
|||
|
|||
@Parameter(names = { "-r", "--deep" }, description = "generate SDBFs from directories and files") |
|||
private boolean goDeep = false; |
|||
|
|||
@Parameter(names = { "-g", "--gen-compare" }, description = "generate SDBFs and compare all pairs") |
|||
private boolean genCompare = false; |
|||
|
|||
@Parameter(names = { "-p", "--threads" }, description = "compute threads to use") |
|||
public Integer threads = SystemInfo.LogicalCores; |
|||
|
|||
public Integer minhashSize = 1024; |
|||
|
|||
/** |
|||
* This will hold the indexes we are supposed to compare |
|||
*/ |
|||
@Parameter(names = { "-c", "--compare" }, description = "compare all pairs in SDBF file, or compare two SDBF files to each other") |
|||
private boolean toCompare = false; |
|||
|
|||
@Parameter(names = { "-o", "--output" }, description = "send output to files", converter = FileConverter.class) |
|||
public File alt_output = new File(""); |
|||
|
|||
/** |
|||
* This will hold default inputs we should parse |
|||
*/ |
|||
@Parameter(converter = FileConverter.class) |
|||
private List<File> parameters = new ArrayList<>(); |
|||
|
|||
|
|||
//Tools used for parallel execution
|
|||
private static ExecutorService ex; |
|||
/** |
|||
* Multiplier applied to the number of problem sub-components created. Done |
|||
* so that work-stealing pool can do load balancing for us |
|||
*/ |
|||
private static final int P_MUL = 500; |
|||
private static final ReentrantLock stdOutLock = new ReentrantLock(); |
|||
/** |
|||
* This list provides a place for ALL StringBuilders used by any and all |
|||
* threads. |
|||
*/ |
|||
private static final ConcurrentLinkedQueue<StringBuilder> localOutPuts = new ConcurrentLinkedQueue<>(); |
|||
/** |
|||
* Access to thread local string builder to place text you want to put to |
|||
* STD out, but can't because its under contention |
|||
*/ |
|||
private static final ThreadLocal<StringBuilder> localToStdOut = ThreadLocal.withInitial(() -> |
|||
{ |
|||
StringBuilder sb = new StringBuilder(); |
|||
localOutPuts.add(sb); |
|||
return sb; |
|||
}); |
|||
|
|||
|
|||
public static void main(String... args) throws IOException, InterruptedException |
|||
{ |
|||
new Main().run(args); |
|||
} |
|||
|
|||
public void run(String... args) throws IOException, InterruptedException |
|||
{ |
|||
JCommander jc = new JCommander(this); |
|||
jc.parse(args); |
|||
ex = Executors.newWorkStealingPool(Math.max(1, threads)); |
|||
if(!alt_output.getPath().equals("")) |
|||
System.setOut(new PrintStream(new BufferedOutputStream(new FileOutputStream(alt_output)), true)); |
|||
|
|||
//collect all the files we will be hashing
|
|||
List<File> toHash = new ArrayList<>(); |
|||
for(File candidate : parameters) |
|||
if(candidate.isFile()) |
|||
toHash.add(candidate); |
|||
else if(candidate.isDirectory() && goDeep) |
|||
Files.walk(candidate.toPath()).filter(Files::isRegularFile).forEach(c -> toHash.add(c.toFile())); |
|||
|
|||
if(toCompare) |
|||
{ |
|||
if(parameters.size() > 2 || parameters.isEmpty()) |
|||
throw new IllegalArgumentException("Can only compare at most two indexes at a time!"); |
|||
|
|||
List<int[]> hashesA = new ArrayList<>(); |
|||
List<String> filesA = new ArrayList<>(); |
|||
|
|||
List<int[]> hashesB = new ArrayList<>(); |
|||
List<String> filesB = new ArrayList<>(); |
|||
|
|||
readHashesFromFile(parameters.get(0), hashesA, filesA); |
|||
if(parameters.size() == 2) |
|||
readHashesFromFile(parameters.get(1), hashesB, filesB); |
|||
else |
|||
{ |
|||
hashesB = hashesA; |
|||
filesB = filesA; |
|||
} |
|||
|
|||
compare(hashesA, filesA, hashesB, filesB); |
|||
} |
|||
else if(genCompare) |
|||
genComp(toHash); |
|||
else |
|||
hashFiles(toHash); |
|||
|
|||
ex.shutdownNow(); |
|||
} |
|||
|
|||
/** |
|||
* Perform comparisons of the given digests lists. If each list points to |
|||
* the same object, only the above-diagonal elements of the comparison |
|||
* matrix will be performed |
|||
* |
|||
* @param hashesA the list of min-hashes for the first set, ordered |
|||
* @param filesA the list of file names for the first set, ordered |
|||
* @param hashesB the list of min-hashes for the second set, ordered |
|||
* @param filesB the list of file names for the first set, ordered |
|||
* @throws InterruptedException |
|||
*/ |
|||
public void compare(List<int[]> hashesA, List<String> filesA, List<int[]> hashesB, List<String> filesB) throws InterruptedException |
|||
{ |
|||
CountDownLatch latch = new CountDownLatch(hashesA.size()); |
|||
for(int i = 0; i < hashesA.size(); i++) |
|||
{ |
|||
int[] hAiH = hashesA.get(i); |
|||
String hAiN = filesA.get(i); |
|||
int j_start; |
|||
if(hashesA == hashesB) |
|||
j_start = i+1;//don't self compare / repeat comparisons
|
|||
else |
|||
j_start = 0; |
|||
|
|||
ex.submit(() -> |
|||
{ |
|||
for(int j = j_start; j < hashesB.size(); j++) |
|||
{ |
|||
int sim = (int) Math.round(100*LZJDf.similarity(hAiH, hashesB.get(j))); |
|||
if(sim >= threshold) |
|||
{ |
|||
StringBuilder toPrint = localToStdOut.get(); |
|||
toPrint.append(String.format(hAiN + "|" + filesB.get(j) + "|%03d\n", sim)); |
|||
|
|||
tryPrint(toPrint); |
|||
} |
|||
} |
|||
latch.countDown(); |
|||
}); |
|||
} |
|||
|
|||
latch.await(); |
|||
printAllLocalBuffers(); |
|||
} |
|||
|
|||
private void readHashesFromFile(File f, List<int[]> hashesA, List<String> files) throws IOException |
|||
{ |
|||
try(BufferedReader br = new BufferedReader(new FileReader(f))) |
|||
{ |
|||
String line; |
|||
while((line = br.readLine()) != null) |
|||
{ |
|||
line = line.trim(); |
|||
if(line.isEmpty()) |
|||
continue; |
|||
int colonIndx = line.lastIndexOf(":"); |
|||
String name = line.substring("lzjd:".length(), colonIndx); |
|||
String b64 = line.substring(colonIndx+1); |
|||
|
|||
byte[] cmp = Base64.getDecoder().decode(b64); |
|||
int hashLen = cmp.length/Integer.SIZE; |
|||
int[] hash = new int[hashLen]; |
|||
IntBuffer readBack = ByteBuffer.wrap(cmp).asIntBuffer(); |
|||
for(int i = 0; i < hash.length; i++) |
|||
hash[i] = readBack.get(i); |
|||
|
|||
hashesA.add(hash); |
|||
files.add(name); |
|||
} |
|||
} |
|||
} |
|||
|
|||
/** |
|||
* Digest and print out the hashes for the given list of files |
|||
* @param toHash the list of files to digest |
|||
* @throws IOException |
|||
* @throws InterruptedException |
|||
*/ |
|||
private void hashFiles(List<File> toHash) throws IOException, InterruptedException |
|||
{ |
|||
ThreadLocal<byte[]> localTmpSpace = ThreadLocal.withInitial(()->new byte[minhashSize*Integer.BYTES]); |
|||
CountDownLatch latch = new CountDownLatch(SystemInfo.LogicalCores*P_MUL); |
|||
IntStream.range(0, SystemInfo.LogicalCores * P_MUL).forEach(id-> |
|||
{ |
|||
ex.submit(() -> |
|||
{ |
|||
for (int i = id; i < toHash.size(); i += SystemInfo.LogicalCores * P_MUL) |
|||
{ |
|||
try |
|||
{ |
|||
File f = toHash.get(i); |
|||
LZJDf.min_hashes.clear();//hacky, but I don't really care
|
|||
int[] hash = LZJDf.getMinHash(-1, f, (int) Math.min(minhashSize, f.length()/2)); |
|||
|
|||
byte[] byte_tmp_space = localTmpSpace.get(); |
|||
ByteBuffer byteBuffer = ByteBuffer.wrap(byte_tmp_space); |
|||
IntBuffer intBuffer = byteBuffer.asIntBuffer(); |
|||
intBuffer.put(hash); |
|||
|
|||
String b64 = Base64.getEncoder().encodeToString(byte_tmp_space); |
|||
|
|||
StringBuilder toPrint = localToStdOut.get(); |
|||
toPrint.append("lzjd:").append(f.toString()).append(":").append(b64).append("\n"); |
|||
|
|||
tryPrint(toPrint); |
|||
} |
|||
catch (IOException ex1) |
|||
{ |
|||
Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex1); |
|||
} |
|||
} |
|||
latch.countDown(); |
|||
}); |
|||
}); |
|||
|
|||
latch.await(); |
|||
printAllLocalBuffers(); |
|||
} |
|||
|
|||
/** |
|||
* Go through every local string buffer and pring them all to std out. |
|||
*/ |
|||
public void printAllLocalBuffers() |
|||
{ |
|||
for(StringBuilder sb: localOutPuts)//make sure we print off everything!
|
|||
{ |
|||
System.out.print(sb.toString()); |
|||
sb.setLength(0); |
|||
} |
|||
} |
|||
|
|||
/** |
|||
* This will attempt to print out the locally built buffer of lines to send |
|||
* to STD out. Will update toPrint as appropriate if the attempt was |
|||
* successful |
|||
* |
|||
* @param toPrint the string buffer to print out |
|||
*/ |
|||
public void tryPrint(StringBuilder toPrint) |
|||
{ |
|||
if(stdOutLock.tryLock()) |
|||
{ |
|||
System.out.print(toPrint.toString()); |
|||
toPrint.setLength(0); |
|||
stdOutLock.unlock(); |
|||
} |
|||
else if(toPrint.length() > 1024*1024*10)//you have 10MB worth of ASCII? Just print already!
|
|||
{ |
|||
stdOutLock.lock(); |
|||
try |
|||
{ |
|||
System.out.print(toPrint.toString()); |
|||
toPrint.setLength(0); |
|||
} |
|||
finally |
|||
{ |
|||
stdOutLock.unlock(); |
|||
} |
|||
} |
|||
} |
|||
|
|||
/** |
|||
* Generate the set of digests and do the all pairs comparison at the same |
|||
* time. |
|||
* |
|||
* @param toHash the list of files to digest and compare |
|||
* @throws IOException |
|||
* @throws InterruptedException |
|||
*/ |
|||
private void genComp(List<File> toHash) throws IOException, InterruptedException |
|||
{ |
|||
int[][] hashes = new int[toHash.size()][minhashSize]; |
|||
String[] names = new String[toHash.size()]; |
|||
|
|||
CountDownLatch latch = new CountDownLatch(SystemInfo.LogicalCores * P_MUL); |
|||
IntStream.range(0, SystemInfo.LogicalCores * P_MUL).forEach(id-> |
|||
{ |
|||
ex.submit(() -> |
|||
{ |
|||
for (int i = id; i < toHash.size(); i += SystemInfo.LogicalCores * P_MUL) |
|||
{ |
|||
try |
|||
{ |
|||
File f = toHash.get(i); |
|||
LZJDf.min_hashes.clear(); |
|||
int[] hash = LZJDf.getMinHash(-1, f, minhashSize); |
|||
hashes[i] = hash; |
|||
names[i] = f.toString(); |
|||
} |
|||
catch (IOException ex1) |
|||
{ |
|||
Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex1); |
|||
} |
|||
} |
|||
latch.countDown(); |
|||
}); |
|||
}); |
|||
|
|||
|
|||
latch.await(); |
|||
|
|||
List<int[]> hashList = Arrays.asList(hashes); |
|||
List<String> nameList = Arrays.asList(names); |
|||
|
|||
compare(hashList, nameList, hashList, nameList); |
|||
} |
|||
} |
@ -0,0 +1,410 @@ |
|||
package com.edwardraff.jlzjd; |
|||
|
|||
/** |
|||
* The MurmurHash3 algorithm was created by Austin Appleby and placed in the public domain. |
|||
* This java port was authored by Yonik Seeley and also placed into the public domain. |
|||
* The author hereby disclaims copyright to this source code. |
|||
* <p> |
|||
* This produces exactly the same hash values as the final C++ |
|||
* version of MurmurHash3 and is thus suitable for producing the same hash values across |
|||
* platforms. |
|||
* <p> |
|||
* The 32 bit x86 version of this hash should be the fastest variant for relatively short keys like ids. |
|||
* murmurhash3_x64_128 is a good choice for longer strings or if you need more than 32 bits of hash. |
|||
* <p> |
|||
* Note - The x86 and x64 versions do _not_ produce the same results, as the |
|||
* algorithms are optimized for their respective platforms. |
|||
* <p> |
|||
* See http://github.com/yonik/java_util for future updates to this file.
|
|||
*/ |
|||
public final class MurmurHash3 |
|||
{ |
|||
/** |
|||
* the length of the current running byte sequence |
|||
*/ |
|||
private int _len; |
|||
/** |
|||
* the byte history for the last 4 bytes seen |
|||
*/ |
|||
private final byte[] data = new byte[4]; |
|||
private int _h1; |
|||
private int _seed = 0; |
|||
|
|||
public MurmurHash3() |
|||
{ |
|||
this(0); |
|||
} |
|||
|
|||
public MurmurHash3(int seed) |
|||
{ |
|||
this._seed = seed; |
|||
reset(); |
|||
} |
|||
|
|||
public void reset() |
|||
{ |
|||
_len = 0; |
|||
_h1 = _seed; |
|||
} |
|||
|
|||
public int pushByte(byte b) |
|||
{ |
|||
//store the current byte of input
|
|||
data[_len % 4] = b; |
|||
_len++; |
|||
|
|||
final int c1 = 0xcc9e2d51; |
|||
final int c2 = 0x1b873593; |
|||
|
|||
// int h1 = seed;
|
|||
// int roundedEnd = offset + (len & 0xfffffffc); // round down to 4 byte block
|
|||
|
|||
/** |
|||
* We will use this as the value of _h1 to dirty for returning to the caller |
|||
*/ |
|||
int h1_as_if_done; |
|||
if(_len > 0 && _len % 4 == 0)//we have a valid history of 4 items!
|
|||
{ |
|||
// little endian load order
|
|||
int k1 = (data[0] & 0xff) | ((data[1] & 0xff) << 8) | ((data[2] & 0xff) << 16) | (data[3] << 24); |
|||
k1 *= c1; |
|||
k1 = (k1 << 15) | (k1 >>> 17); // ROTL32(k1,15);
|
|||
k1 *= c2; |
|||
|
|||
_h1 ^= k1; |
|||
_h1 = (_h1 << 13) | (_h1 >>> 19); // ROTL32(h1,13);
|
|||
_h1 = _h1*5+0xe6546b64; |
|||
h1_as_if_done = _h1; |
|||
} |
|||
else//tail case
|
|||
{ |
|||
// tail
|
|||
int k1 = 0; |
|||
h1_as_if_done = _h1; |
|||
|
|||
switch(_len & 0x03) { |
|||
case 3: |
|||
k1 = (data[2] & 0xff) << 16; |
|||
// fallthrough
|
|||
case 2: |
|||
k1 |= (data[1] & 0xff) << 8; |
|||
// fallthrough
|
|||
case 1: |
|||
k1 |= (data[0] & 0xff); |
|||
k1 *= c1; |
|||
k1 = (k1 << 15) | (k1 >>> 17); // ROTL32(k1,15);
|
|||
k1 *= c2; |
|||
h1_as_if_done ^= k1; |
|||
} |
|||
} |
|||
|
|||
// finalization
|
|||
h1_as_if_done ^= _len; |
|||
|
|||
// fmix(h1);
|
|||
h1_as_if_done ^= h1_as_if_done >>> 16; |
|||
h1_as_if_done *= 0x85ebca6b; |
|||
h1_as_if_done ^= h1_as_if_done >>> 13; |
|||
h1_as_if_done *= 0xc2b2ae35; |
|||
h1_as_if_done ^= h1_as_if_done >>> 16; |
|||
|
|||
return h1_as_if_done; |
|||
} |
|||
|
|||
/** 128 bits of state */ |
|||
public static final class LongPair { |
|||
public long val1; |
|||
public long val2; |
|||
} |
|||
|
|||
public static final int fmix32(int h) { |
|||
h ^= h >>> 16; |
|||
h *= 0x85ebca6b; |
|||
h ^= h >>> 13; |
|||
h *= 0xc2b2ae35; |
|||
h ^= h >>> 16; |
|||
return h; |
|||
} |
|||
|
|||
public static final long fmix64(long k) { |
|||
k ^= k >>> 33; |
|||
k *= 0xff51afd7ed558ccdL; |
|||
k ^= k >>> 33; |
|||
k *= 0xc4ceb9fe1a85ec53L; |
|||
k ^= k >>> 33; |
|||
return k; |
|||
} |
|||
|
|||
/** Gets a long from a byte buffer in little endian byte order. */ |
|||
public static final long getLongLittleEndian(byte[] buf, int offset) { |
|||
return ((long)buf[offset+7] << 56) // no mask needed
|
|||
| ((buf[offset+6] & 0xffL) << 48) |
|||
| ((buf[offset+5] & 0xffL) << 40) |
|||
| ((buf[offset+4] & 0xffL) << 32) |
|||
| ((buf[offset+3] & 0xffL) << 24) |
|||
| ((buf[offset+2] & 0xffL) << 16) |
|||
| ((buf[offset+1] & 0xffL) << 8) |
|||
| ((buf[offset ] & 0xffL)); // no shift needed
|
|||
} |
|||
|
|||
/** |
|||
* Returns the MurmurHash3_x86_32 hash. Uses a seed of 0. |
|||
* |
|||
* @param data the data to hash |
|||
* @param offset the starting index to begin hashing from |
|||
* @param len the length in bytes of the sequence to hash |
|||
* @return the final hash output value |
|||
*/ |
|||
public static int murmurhash3_x86_32(byte[] data, int offset, int len) |
|||
{ |
|||
return murmurhash3_x86_32(data, offset, len, 0); |
|||
} |
|||
/** |
|||
* Returns the MurmurHash3_x86_32 hash. |
|||
* |
|||
* @param data the data to hash |
|||
* @param offset the starting index to begin hashing from |
|||
* @param len the length in bytes of the sequence to hash |
|||
* @param seed the seed to use for hashing |
|||
* @return the final hash output value |
|||
*/ |
|||
public static int murmurhash3_x86_32(byte[] data, int offset, int len, int seed) |
|||
{ |
|||
final int c1 = 0xcc9e2d51; |
|||
final int c2 = 0x1b873593; |
|||
|
|||
int h1 = seed; |
|||
int roundedEnd = offset + (len & 0xfffffffc); // round down to 4 byte block
|
|||
|
|||
for (int i=offset; i<roundedEnd; i+=4) { |
|||
// little endian load order
|
|||
int k1 = (data[i] & 0xff) | ((data[i+1] & 0xff) << 8) | ((data[i+2] & 0xff) << 16) | (data[i+3] << 24); |
|||
k1 *= c1; |
|||
k1 = (k1 << 15) | (k1 >>> 17); // ROTL32(k1,15);
|
|||
k1 *= c2; |
|||
|
|||
h1 ^= k1; |
|||
h1 = (h1 << 13) | (h1 >>> 19); // ROTL32(h1,13);
|
|||
h1 = h1*5+0xe6546b64; |
|||
} |
|||
|
|||
// tail
|
|||
int k1 = 0; |
|||
|
|||
switch(len & 0x03) { |
|||
case 3: |
|||
k1 = (data[roundedEnd + 2] & 0xff) << 16; |
|||
// fallthrough
|
|||
case 2: |
|||
k1 |= (data[roundedEnd + 1] & 0xff) << 8; |
|||
// fallthrough
|
|||
case 1: |
|||
k1 |= (data[roundedEnd] & 0xff); |
|||
k1 *= c1; |
|||
k1 = (k1 << 15) | (k1 >>> 17); // ROTL32(k1,15);
|
|||
k1 *= c2; |
|||
h1 ^= k1; |
|||
} |
|||
|
|||
// finalization
|
|||
h1 ^= len; |
|||
|
|||
// fmix(h1);
|
|||
h1 ^= h1 >>> 16; |
|||
h1 *= 0x85ebca6b; |
|||
h1 ^= h1 >>> 13; |
|||
h1 *= 0xc2b2ae35; |
|||
h1 ^= h1 >>> 16; |
|||
|
|||
return h1; |
|||
} |
|||
|
|||
|
|||
/** Returns the MurmurHash3_x86_32 hash of the UTF-8 bytes of the String without actually encoding |
|||
* the string to a temporary buffer. This is more than 2x faster than hashing the result |
|||
* of String.getBytes(). |
|||
*/ |
|||
public static int murmurhash3_x86_32(CharSequence data, int offset, int len, int seed) { |
|||
|
|||
final int c1 = 0xcc9e2d51; |
|||
final int c2 = 0x1b873593; |
|||
|
|||
int h1 = seed; |
|||
|
|||
int pos = offset; |
|||
int end = offset + len; |
|||
int k1 = 0; |
|||
int k2 = 0; |
|||
int shift = 0; |
|||
int bits = 0; |
|||
int nBytes = 0; // length in UTF8 bytes
|
|||
|
|||
|
|||
while (pos < end) { |
|||
int code = data.charAt(pos++); |
|||
if (code < 0x80) { |
|||
k2 = code; |
|||
bits = 8; |
|||
|
|||
/*** |
|||
// optimized ascii implementation (currently slower!!! code size?)
|
|||
if (shift == 24) { |
|||
k1 = k1 | (code << 24); |
|||
|
|||
k1 *= c1; |
|||
k1 = (k1 << 15) | (k1 >>> 17); // ROTL32(k1,15);
|
|||
k1 *= c2; |
|||
|
|||
h1 ^= k1; |
|||
h1 = (h1 << 13) | (h1 >>> 19); // ROTL32(h1,13);
|
|||
h1 = h1*5+0xe6546b64; |
|||
|
|||
shift = 0; |
|||
nBytes += 4; |
|||
k1 = 0; |
|||
} else { |
|||
k1 |= code << shift; |
|||
shift += 8; |
|||
} |
|||
continue; |
|||
***/ |
|||
|
|||
} |
|||
else if (code < 0x800) { |
|||
k2 = (0xC0 | (code >> 6)) |
|||
| ((0x80 | (code & 0x3F)) << 8); |
|||
bits = 16; |
|||
} |
|||
else if (code < 0xD800 || code > 0xDFFF || pos>=end) { |
|||
// we check for pos>=end to encode an unpaired surrogate as 3 bytes.
|
|||
k2 = (0xE0 | (code >> 12)) |
|||
| ((0x80 | ((code >> 6) & 0x3F)) << 8) |
|||
| ((0x80 | (code & 0x3F)) << 16); |
|||
bits = 24; |
|||
} else { |
|||
// surrogate pair
|
|||
// int utf32 = pos < end ? (int) data.charAt(pos++) : 0;
|
|||
int utf32 = (int) data.charAt(pos++); |
|||
utf32 = ((code - 0xD7C0) << 10) + (utf32 & 0x3FF); |
|||
k2 = (0xff & (0xF0 | (utf32 >> 18))) |
|||
| ((0x80 | ((utf32 >> 12) & 0x3F))) << 8 |
|||
| ((0x80 | ((utf32 >> 6) & 0x3F))) << 16 |
|||
| (0x80 | (utf32 & 0x3F)) << 24; |
|||
bits = 32; |
|||
} |
|||
|
|||
|
|||
k1 |= k2 << shift; |
|||
|
|||
// int used_bits = 32 - shift; // how many bits of k2 were used in k1.
|
|||
// int unused_bits = bits - used_bits; // (bits-(32-shift)) == bits+shift-32 == bits-newshift
|
|||
|
|||
shift += bits; |
|||
if (shift >= 32) { |
|||
// mix after we have a complete word
|
|||
|
|||
k1 *= c1; |
|||
k1 = (k1 << 15) | (k1 >>> 17); // ROTL32(k1,15);
|
|||
k1 *= c2; |
|||
|
|||
h1 ^= k1; |
|||
h1 = (h1 << 13) | (h1 >>> 19); // ROTL32(h1,13);
|
|||
h1 = h1*5+0xe6546b64; |
|||
|
|||
shift -= 32; |
|||
// unfortunately, java won't let you shift 32 bits off, so we need to check for 0
|
|||
if (shift != 0) { |
|||
k1 = k2 >>> (bits-shift); // bits used == bits - newshift
|
|||
} else { |
|||
k1 = 0; |
|||
} |
|||
nBytes += 4; |
|||
} |
|||
|
|||
} // inner
|
|||
|
|||
// handle tail
|
|||
if (shift > 0) { |
|||
nBytes += shift >> 3; |
|||
k1 *= c1; |
|||
k1 = (k1 << 15) | (k1 >>> 17); // ROTL32(k1,15);
|
|||
k1 *= c2; |
|||
h1 ^= k1; |
|||
} |
|||
|
|||
// finalization
|
|||
h1 ^= nBytes; |
|||
|
|||
// fmix(h1);
|
|||
h1 ^= h1 >>> 16; |
|||
h1 *= 0x85ebca6b; |
|||
h1 ^= h1 >>> 13; |
|||
h1 *= 0xc2b2ae35; |
|||
h1 ^= h1 >>> 16; |
|||
|
|||
return h1; |
|||
} |
|||
|
|||
|
|||
/** Returns the MurmurHash3_x64_128 hash, placing the result in "out". */ |
|||
public static void murmurhash3_x64_128(byte[] key, int offset, int len, int seed, LongPair out) { |
|||
// The original algorithm does have a 32 bit unsigned seed.
|
|||
// We have to mask to match the behavior of the unsigned types and prevent sign extension.
|
|||
long h1 = seed & 0x00000000FFFFFFFFL; |
|||
long h2 = seed & 0x00000000FFFFFFFFL; |
|||
|
|||
final long c1 = 0x87c37b91114253d5L; |
|||
final long c2 = 0x4cf5ad432745937fL; |
|||
|
|||
int roundedEnd = offset + (len & 0xFFFFFFF0); // round down to 16 byte block
|
|||
for (int i=offset; i<roundedEnd; i+=16) { |
|||
long k1 = getLongLittleEndian(key, i); |
|||
long k2 = getLongLittleEndian(key, i+8); |
|||
k1 *= c1; k1 = Long.rotateLeft(k1,31); k1 *= c2; h1 ^= k1; |
|||
h1 = Long.rotateLeft(h1,27); h1 += h2; h1 = h1*5+0x52dce729; |
|||
k2 *= c2; k2 = Long.rotateLeft(k2,33); k2 *= c1; h2 ^= k2; |
|||
h2 = Long.rotateLeft(h2,31); h2 += h1; h2 = h2*5+0x38495ab5; |
|||
} |
|||
|
|||
long k1 = 0; |
|||
long k2 = 0; |
|||
|
|||
switch (len & 15) { |
|||
case 15: k2 = (key[roundedEnd+14] & 0xffL) << 48; |
|||
case 14: k2 |= (key[roundedEnd+13] & 0xffL) << 40; |
|||
case 13: k2 |= (key[roundedEnd+12] & 0xffL) << 32; |
|||
case 12: k2 |= (key[roundedEnd+11] & 0xffL) << 24; |
|||
case 11: k2 |= (key[roundedEnd+10] & 0xffL) << 16; |
|||
case 10: k2 |= (key[roundedEnd+ 9] & 0xffL) << 8; |
|||
case 9: k2 |= (key[roundedEnd+ 8] & 0xffL); |
|||
k2 *= c2; k2 = Long.rotateLeft(k2, 33); k2 *= c1; h2 ^= k2; |
|||
case 8: k1 = ((long)key[roundedEnd+7]) << 56; |
|||
case 7: k1 |= (key[roundedEnd+6] & 0xffL) << 48; |
|||
case 6: k1 |= (key[roundedEnd+5] & 0xffL) << 40; |
|||
case 5: k1 |= (key[roundedEnd+4] & 0xffL) << 32; |
|||
case 4: k1 |= (key[roundedEnd+3] & 0xffL) << 24; |
|||
case 3: k1 |= (key[roundedEnd+2] & 0xffL) << 16; |
|||
case 2: k1 |= (key[roundedEnd+1] & 0xffL) << 8; |
|||
case 1: k1 |= (key[roundedEnd ] & 0xffL); |
|||
k1 *= c1; k1 = Long.rotateLeft(k1,31); k1 *= c2; h1 ^= k1; |
|||
} |
|||
|
|||
//----------
|
|||
// finalization
|
|||
|
|||
h1 ^= len; h2 ^= len; |
|||
|
|||
h1 += h2; |
|||
h2 += h1; |
|||
|
|||
h1 = fmix64(h1); |
|||
h2 = fmix64(h2); |
|||
|
|||
h1 += h2; |
|||
h2 += h1; |
|||
|
|||
out.val1 = h1; |
|||
out.val2 = h2; |
|||
} |
|||
|
|||
} |
@ -0,0 +1,66 @@ |
|||
/* |
|||
* To change this license header, choose License Headers in Project Properties. |
|||
* To change this template file, choose Tools | Templates |
|||
* and open the template in the editor. |
|||
*/ |
|||
package com.edwardraff.jlzjd; |
|||
|
|||
import java.util.Random; |
|||
import jsat.utils.random.XORWOW; |
|||
import org.junit.After; |
|||
import org.junit.AfterClass; |
|||
import org.junit.Before; |
|||
import org.junit.BeforeClass; |
|||
import org.junit.Test; |
|||
import static org.junit.Assert.*; |
|||
|
|||
/** |
|||
* |
|||
* @author Edward Raff |
|||
*/ |
|||
public class MurmurHash3Test |
|||
{ |
|||
|
|||
public MurmurHash3Test() |
|||
{ |
|||
} |
|||
|
|||
@BeforeClass |
|||
public static void setUpClass() |
|||
{ |
|||
} |
|||
|
|||
@AfterClass |
|||
public static void tearDownClass() |
|||
{ |
|||
} |
|||
|
|||
@Before |
|||
public void setUp() |
|||
{ |
|||
} |
|||
|
|||
@After |
|||
public void tearDown() |
|||
{ |
|||
} |
|||
|
|||
/** |
|||
* Test of pushByte method, of class MurmurHash3. |
|||
*/ |
|||
@org.junit.Test |
|||
public void testPushByte() |
|||
{ |
|||
System.out.println("pushByte"); |
|||
Random rand = new XORWOW(); |
|||
int seed = rand.nextInt(); |
|||
MurmurHash3 instance = new MurmurHash3(seed); |
|||
|
|||
byte[] bytes = new byte[4096]; |
|||
rand.nextBytes(bytes); |
|||
|
|||
for(int i = 0; i < bytes.length; i++) |
|||
assertEquals("Failed on " + i, MurmurHash3.murmurhash3_x86_32(bytes, 0, i+1, seed), instance.pushByte(bytes[i])); |
|||
} |
|||
|
|||
} |
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@ -0,0 +1,5 @@ |
|||
#Generated by Maven |
|||
#Tue Mar 10 11:34:42 EDT 2020 |
|||
groupId=com.edwardraff |
|||
artifactId=jLZJD |
|||
version=1.0-SNAPSHOT |
@ -0,0 +1,6 @@ |
|||
com/edwardraff/jlzjd/IntSetNoRemove.class |
|||
com/edwardraff/jlzjd/MurmurHash3$LongPair.class |
|||
com/edwardraff/jlzjd/Main.class |
|||
com/edwardraff/jlzjd/MurmurHash3.class |
|||
com/edwardraff/jlzjd/LZJDf.class |
|||
com/edwardraff/jlzjd/IntSetNoRemove$1.class |
@ -0,0 +1,4 @@ |
|||
/Users/hrbrmstr/packages/lizzard/java/lizzard/src/main/java/com/edwardraff/jlzjd/MurmurHash3.java |
|||
/Users/hrbrmstr/packages/lizzard/java/lizzard/src/main/java/com/edwardraff/jlzjd/LZJDf.java |
|||
/Users/hrbrmstr/packages/lizzard/java/lizzard/src/main/java/com/edwardraff/jlzjd/IntSetNoRemove.java |
|||
/Users/hrbrmstr/packages/lizzard/java/lizzard/src/main/java/com/edwardraff/jlzjd/Main.java |
@ -0,0 +1 @@ |
|||
com/edwardraff/jlzjd/MurmurHash3Test.class |
@ -0,0 +1 @@ |
|||
/Users/hrbrmstr/packages/lizzard/java/lizzard/src/test/java/com/edwardraff/jlzjd/MurmurHash3Test.java |
@ -0,0 +1,69 @@ |
|||
<?xml version="1.0" encoding="UTF-8" ?> |
|||
<testsuite tests="1" failures="0" name="com.edwardraff.jlzjd.MurmurHash3Test" time="0.021" errors="0" skipped="0"> |
|||
<properties> |
|||
<property name="java.runtime.name" value="Java(TM) SE Runtime Environment"/> |
|||
<property name="java.vm.version" value="11.0.1+13-LTS"/> |
|||
<property name="sun.boot.library.path" value="/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib"/> |
|||
<property name="gopherProxySet" value="false"/> |
|||
<property name="maven.multiModuleProjectDirectory" value="/Users/hrbrmstr/packages/lizzard/java/lizzard"/> |
|||
<property name="java.vm.vendor" value="Oracle Corporation"/> |
|||
<property name="java.vendor.url" value="http://java.oracle.com/"/> |
|||
<property name="guice.disable.misplaced.annotation.check" value="true"/> |
|||
<property name="path.separator" value=":"/> |
|||
<property name="java.vm.name" value="Java HotSpot(TM) 64-Bit Server VM"/> |
|||
<property name="sun.os.patch.level" value="unknown"/> |
|||
<property name="user.country" value="US"/> |
|||
<property name="sun.java.launcher" value="SUN_STANDARD"/> |
|||
<property name="java.vm.specification.name" value="Java Virtual Machine Specification"/> |
|||
<property name="user.dir" value="/Users/hrbrmstr/packages/lizzard/java/lizzard"/> |
|||
<property name="java.vm.compressedOopsMode" value="Zero based"/> |
|||
<property name="java.runtime.version" value="11.0.1+13-LTS"/> |
|||
<property name="java.awt.graphicsenv" value="sun.awt.CGraphicsEnvironment"/> |
|||
<property name="os.arch" value="x86_64"/> |
|||
<property name="java.io.tmpdir" value="/var/folders/1w/2d82v7ts3gs98tc6v772h8s40000gp/T/"/> |
|||
<property name="line.separator" value=" |
|||
"/> |
|||
<property name="java.vm.specification.vendor" value="Oracle Corporation"/> |
|||
<property name="os.name" value="Mac OS X"/> |
|||
<property name="classworlds.conf" value="/usr/local/Cellar/maven/3.6.3_1/libexec/bin/m2.conf"/> |
|||
<property name="sun.jnu.encoding" value="UTF-8"/> |
|||
<property name="java.library.path" value="/Users/hrbrmstr/Library/Java/Extensions:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java:."/> |
|||
<property name="maven.conf" value="/usr/local/Cellar/maven/3.6.3_1/libexec/conf"/> |
|||
<property name="jdk.debug" value="release"/> |
|||
<property name="java.class.version" value="55.0"/> |
|||
<property name="java.specification.name" value="Java Platform API Specification"/> |
|||
<property name="sun.management.compiler" value="HotSpot 64-Bit Tiered Compilers"/> |
|||
<property name="os.version" value="10.15.4"/> |
|||
<property name="library.jansi.path" value="/usr/local/Cellar/maven/3.6.3_1/libexec/lib/jansi-native"/> |
|||
<property name="http.nonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/> |
|||
<property name="user.home" value="/Users/hrbrmstr"/> |
|||
<property name="user.timezone" value="America/New_York"/> |
|||
<property name="java.awt.printerjob" value="sun.lwawt.macosx.CPrinterJob"/> |
|||
<property name="file.encoding" value="UTF-8"/> |
|||
<property name="java.specification.version" value="11"/> |
|||
<property name="user.name" value="hrbrmstr"/> |
|||
<property name="java.class.path" value="/usr/local/Cellar/maven/3.6.3_1/libexec/boot/plexus-classworlds-2.6.0.jar"/> |
|||
<property name="org.slf4j.simpleLogger.defaultLogLevel" value="error"/> |
|||
<property name="java.vm.specification.version" value="11"/> |
|||
<property name="sun.arch.data.model" value="64"/> |
|||
<property name="sun.java.command" value="org.codehaus.plexus.classworlds.launcher.Launcher --quiet package"/> |
|||
<property name="java.home" value="/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home"/> |
|||
<property name="user.language" value="en"/> |
|||
<property name="java.specification.vendor" value="Oracle Corporation"/> |
|||
<property name="awt.toolkit" value="sun.lwawt.macosx.LWCToolkit"/> |
|||
<property name="java.vm.info" value="mixed mode"/> |
|||
<property name="java.version" value="11.0.1"/> |
|||
<property name="java.vendor" value="Oracle Corporation"/> |
|||
<property name="maven.home" value="/usr/local/Cellar/maven/3.6.3_1/libexec"/> |
|||
<property name="file.separator" value="/"/> |
|||
<property name="java.version.date" value="2018-10-16"/> |
|||
<property name="java.vendor.url.bug" value="http://bugreport.java.com/bugreport/"/> |
|||
<property name="sun.io.unicode.encoding" value="UnicodeBig"/> |
|||
<property name="sun.cpu.endian" value="little"/> |
|||
<property name="java.vendor.version" value="18.9"/> |
|||
<property name="socksNonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/> |
|||
<property name="ftp.nonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/> |
|||
<property name="sun.cpu.isalist" value=""/> |
|||
</properties> |
|||
<testcase classname="com.edwardraff.jlzjd.MurmurHash3Test" name="testPushByte" time="0.021"/> |
|||
</testsuite> |
@ -0,0 +1,4 @@ |
|||
------------------------------------------------------------------------------- |
|||
Test set: com.edwardraff.jlzjd.MurmurHash3Test |
|||
------------------------------------------------------------------------------- |
|||
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 sec |
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@ -0,0 +1,19 @@ |
|||
% Generated by roxygen2: do not edit by hand |
|||
% Please edit documentation in R/min-hash-for-file.R |
|||
\name{as.character.lzjd_hash} |
|||
\alias{as.character.lzjd_hash} |
|||
\title{Turn an \code{lzhd_hash} object into a base 64 encoded string} |
|||
\usage{ |
|||
\method{as.character}{lzjd_hash}(x, ...) |
|||
} |
|||
\arguments{ |
|||
\item{x, }{an \code{lzhd_hash} object} |
|||
|
|||
\item{...}{ignored} |
|||
} |
|||
\value{ |
|||
character |
|||
} |
|||
\description{ |
|||
Turn an \code{lzhd_hash} object into a base 64 encoded string |
|||
} |
@ -0,0 +1,17 @@ |
|||
% Generated by roxygen2: do not edit by hand |
|||
% Please edit documentation in R/min-hash-for-file.R |
|||
\name{as_lzjd_hash} |
|||
\alias{as_lzjd_hash} |
|||
\title{Turn an base 64 encoded LZJD hash into an \code{lzjd_hash} object} |
|||
\usage{ |
|||
as_lzjd_hash(x) |
|||
} |
|||
\arguments{ |
|||
\item{x}{base 64 encoded LZJD} |
|||
} |
|||
\value{ |
|||
\code{lzjd_hash} |
|||
} |
|||
\description{ |
|||
Turn an base 64 encoded LZJD hash into an \code{lzjd_hash} object |
|||
} |
@ -0,0 +1,17 @@ |
|||
% Generated by roxygen2: do not edit by hand |
|||
% Please edit documentation in R/min-hash-for-file.R |
|||
\name{compute_distance} |
|||
\alias{compute_distance} |
|||
\title{Compute the distance between two LZJD hashes} |
|||
\usage{ |
|||
compute_distance(h1, h2) |
|||
} |
|||
\arguments{ |
|||
\item{h1, h2}{LZJD hashes} |
|||
} |
|||
\value{ |
|||
numeric distance value (0-1) |
|||
} |
|||
\description{ |
|||
Compute the distance between two LZJD hashes |
|||
} |
@ -0,0 +1,17 @@ |
|||
% Generated by roxygen2: do not edit by hand |
|||
% Please edit documentation in R/min-hash-for-file.R |
|||
\name{compute_similarity} |
|||
\alias{compute_similarity} |
|||
\title{Compute the similarity between two LZJD hashes} |
|||
\usage{ |
|||
compute_similarity(h1, h2) |
|||
} |
|||
\arguments{ |
|||
\item{h1, h2}{LZJD hashes} |
|||
} |
|||
\value{ |
|||
numeric similarity value (0-1) |
|||
} |
|||
\description{ |
|||
Compute the similarity between two LZJD hashes |
|||
} |
@ -0,0 +1,29 @@ |
|||
% Generated by roxygen2: do not edit by hand |
|||
% Please edit documentation in R/min-hash-for-file.R |
|||
\name{min_hash_for_file} |
|||
\alias{min_hash_for_file} |
|||
\alias{print.lzjd_hash} |
|||
\title{Compute the LZJD hash for a file} |
|||
\usage{ |
|||
min_hash_for_file(path) |
|||
|
|||
\method{print}{lzjd_hash}(x, ...) |
|||
} |
|||
\arguments{ |
|||
\item{path}{path to file (it will be \code{\link[=path.expand]{path.expand()}}ed).} |
|||
|
|||
\item{x, }{an \code{lzhd_hash} object} |
|||
|
|||
\item{...}{ignored} |
|||
} |
|||
\value{ |
|||
a \code{lzjd_hash} object which corresponds to a \code{jsat.classifiers.DataPoint} |
|||
(\url{https://github.com/EdwardRaff/JSAT/blob/master/JSAT/src/jsat/classifiers/DataPoint.java)} |
|||
object which, in this case, is an integer vector. |
|||
} |
|||
\description{ |
|||
Compute the LZJD hash for a file |
|||
} |
|||
\examples{ |
|||
h1 <- min_hash_for_file(system.file("extdat", "index.html", package = "lizzard")) |
|||
} |
Loading…
Reference in new issue