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+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.
+
+ Apache Commons Codec - Icy plugin (http://icy.bioimageanalysis.org/).
+ Copyright (C) 2021 Biological Image Analysis unit, Institut Pasteur
+
+ 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:
+
+ Apache Commons Codec Copyright (C) 2021 Biological Image Analysis unit, Institut Pasteur
+ 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>>.
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..75de83b190075f173f0c5ce3b0f8f3c8ba0ab950
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,84 @@
+<?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>
+
+ <!-- Inherited Icy Parent POM -->
+ <parent>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>parent-pom-plugin</artifactId>
+ <version>1.0.6</version>
+ </parent>
+
+ <!-- Project Information -->
+ <artifactId>matlab-communicator</artifactId>
+ <version>1.0.5</version>
+
+ <packaging>jar</packaging>
+
+ <name>Matlab Communicator</name>
+ <description>Low-level functions for interactive communication between Icy and Matlab.</description>
+ <inceptionYear>2022</inceptionYear>
+
+ <organization>
+ <name>Institut Pasteur</name>
+ <url>https://pasteur.fr</url>
+ </organization>
+
+ <licenses>
+ <license>
+ <name>GNU GPLv3</name>
+ <url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
+ <distribution>repo</distribution>
+ </license>
+ </licenses>
+
+ <developers>
+ <developer>
+ <id>ylemontag</id>
+ <name>Yoann Le Montagner</name>
+ <url>https://icy.bioimageanalysis.org/author/ylemontag/</url>
+ <roles>
+ <role>developer</role>
+ <role>maintainer</role>
+ </roles>
+ </developer>
+ </developers>
+
+ <!-- Project properties -->
+ <properties>
+
+ </properties>
+
+ <!-- Project build configuration -->
+ <build>
+ <plugins>
+ </plugins>
+ </build>
+
+ <!-- List of project's dependencies -->
+ <dependencies>
+ <!-- The core of Icy -->
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>icy-kernel</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>matlab-io</artifactId>
+ <version>2.5.2</version>
+ </dependency>
+
+ </dependencies>
+
+ <!-- Icy Maven repository (to find parent POM) -->
+ <repositories>
+ <repository>
+ <id>icy</id>
+ <name>Icy's Nexus</name>
+ <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ </repository>
+ </repositories>
+</project>
diff --git a/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommandException.java b/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommandException.java
new file mode 100644
index 0000000000000000000000000000000000000000..7ec0184a6c7787a6e2796b9d9258c0cc62d7ca48
--- /dev/null
+++ b/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommandException.java
@@ -0,0 +1,27 @@
+package plugins.ylemontag.matlabcommunicator;
+
+/**
+ *
+ * @author Yoann Le Montagner
+ *
+ * Exception thrown by Matlab interpreters plugins when the execution of a command fails
+ */
+public class MatlabCommandException extends Exception
+{
+ private static final long serialVersionUID = 1L;
+
+ public MatlabCommandException()
+ {
+ super();
+ }
+
+ public MatlabCommandException(String message)
+ {
+ super(message);
+ }
+
+ public MatlabCommandException(Throwable throwable)
+ {
+ super(throwable);
+ }
+}
diff --git a/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon.java b/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon.java
new file mode 100644
index 0000000000000000000000000000000000000000..83f9c2de53e26d2c04d62083e15b1d25e45d0001
--- /dev/null
+++ b/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon.java
@@ -0,0 +1,317 @@
+package plugins.ylemontag.matlabcommunicator;
+
+import icy.common.Version;
+import icy.file.FileUtil;
+import icy.gui.frame.progress.ToolTipFrame;
+import icy.network.NetworkUtil;
+import icy.plugin.PluginDescriptor;
+import icy.plugin.PluginLoader;
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginDaemon;
+import icy.preferences.XMLPreferences;
+import icy.system.thread.ThreadUtil;
+import icy.util.ClassUtil;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ *
+ * @author Yoann Le Montagner
+ *
+ * Deamon plugin used to initialize the Matlab communicator server
+ */
+public class MatlabCommunicatorDeamon extends Plugin implements PluginDaemon
+{
+ private static MatlabCommunicatorServer _instance = null;
+ private static Map<String, MatlabSession> _sessions = new HashMap<String, MatlabSession>();
+ private static Map<String, MatlabInterpreter> _interpreters = new HashMap<String, MatlabInterpreter>();
+ private static final String PLUGIN_DIRECTORY = "plugins/ylemontag/matlabcommunicator";
+ private static final String SOURCE_FOLDER_FILE = PLUGIN_DIRECTORY + "/source_folders.txt";
+
+ private void showInstallMessage()
+ {
+ String message = //TODO: remove the intrusive <br/> in the tooltip
+ "<div style=\"font-weight: bold; font-size: 105%; margin-bottom: 8px;\">" +
+ "You've just install the Matlab communicator plugin" +
+ "</div>" +
+ "<div style=\"margin-bottom: 8px;\">" +
+ "To use this plugin, you have to <strong>configure your Matlab application</strong> in a specific way.<br/>" +
+ "In particular, the following commands must be executed each time you start Matlab:<br/>" +
+ "<tt>>> addpath('/path/to/Icy/plugins/ylemontag/matlabcommunicator');</tt><br/>" +
+ "<tt>>> icy_init();</tt><br/>" +
+ "</div>" +
+ "<div style=\"margin-bottom: 8px;\">" +
+ "This operation can be done automatically using a <tt>startup.m</tt> file " +
+ "(please consult<br/>the Matlab documentation for more details)." +
+ "</div>" +
+ "<div style=\"margin-bottom: 8px;\">" +
+ "These instructions are also mentioned in the <tt>icy_init.m</tt> file, " +
+ "located in the<br/><tt>/path/to/icy/plugins/ylemontag/matlabcommunicator</tt> directory." +
+ "</div>"
+ ;
+ new ToolTipFrame(message, "plugins.ylemontag.matlabcommunicator.MatlabCommunicatorDeamon.InstallMessage");
+ }
+
+ /**
+ * Retrieve the previously registered version number for a MatlabInterpreter plugin
+ */
+ private Version getMatlabFunctionVersion(String className)
+ {
+ try {
+ XMLPreferences node = getPreferences("InterpreterVersions");
+ return new Version(node.get(className, ""));
+ }
+ catch(NumberFormatException err) {}
+ return new Version();
+ }
+
+ /**
+ * Set the version number of a MatlabInterpreter plugin
+ */
+ private void setMatlabFunctionVersion(String className, Version version)
+ {
+ XMLPreferences node = getPreferences("InterpreterVersions");
+ node.put(className, version.toString());
+ }
+
+ /**
+ * Extract a .m file from the jar archive
+ */
+ private void extractMatlabFunction(PluginDescriptor descriptor, String functionName)
+ throws IOException
+ {
+ String fileName = ClassUtil.getPathFromQualifiedName(descriptor.getPackageName()) + "/" + functionName + ".m";
+ InputStream resource = getResourceAsStream(fileName);
+ if(resource==null) {
+ throw new IOException("Cannot found the resource " + fileName);
+ }
+ byte[] buffer = NetworkUtil.download(resource);
+ FileUtil.ensureParentDirExist(fileName);
+ OutputStream file = new FileOutputStream(fileName);
+ file.write(buffer);
+ file.close();
+ }
+
+ /**
+ * List all the Matlab function files contained the plugin folder corresponding
+ * to the given plugin descriptor
+ */
+ private Set<String> getExistingMatlabFunctions(PluginDescriptor descriptor)
+ throws IOException
+ {
+ String folder = ClassUtil.getPathFromQualifiedName(descriptor.getPackageName());
+ ArrayList<String> files = FileUtil.getFileListAsString(folder, false, false, false);
+ Set<String> retVal = new HashSet<String>();
+ for(String f : files) {
+ String extension = FileUtil.getFileExtension(f, false);
+ if(extension.equals("m")) {
+ retVal.add(FileUtil.getFileName(f, false));
+ }
+ }
+ return retVal;
+ }
+
+ /**
+ * Change the extension of a .m file into .m.old
+ */
+ private void deprecateMatlabFunction(PluginDescriptor descriptor, String functionName)
+ throws IOException
+ {
+ String fileName = ClassUtil.getPathFromQualifiedName(descriptor.getPackageName()) + "/" + functionName + ".m";
+ if(FileUtil.exists(fileName)) {
+ FileUtil.rename(fileName, fileName + ".old", false);
+ }
+ }
+
+ /**
+ * Clear the file containing the list of source folders
+ */
+ private void clearSourceFolders()
+ {
+ FileUtil.delete(SOURCE_FOLDER_FILE, false);
+ }
+
+ /**
+ * Register the source folder corresponding to a MatlabInterpreter plugin in
+ * the dedicated file
+ */
+ private void appendSourceFolder(PluginDescriptor descriptor) throws IOException
+ {
+ File folder = new File(ClassUtil.getPathFromQualifiedName(descriptor.getPackageName()));
+ String entry = folder.getAbsolutePath() + "\n";
+ byte[] buffer = entry.getBytes("UTF-8");
+ FileUtil.ensureParentDirExist(SOURCE_FOLDER_FILE);
+ OutputStream file = new FileOutputStream(SOURCE_FOLDER_FILE, true);
+ file.write(buffer);
+ file.close();
+ }
+
+ /**
+ * Clear the list of interpreters
+ */
+ private void clearInterpreterInstances()
+ {
+ synchronized (_interpreters) {
+ _interpreters.clear();
+ }
+ }
+
+ /**
+ * Register a plugin instance in the MatlabInterpreter index
+ */
+ private void appendInterpreterInstance(String className, MatlabInterpreter interpreter)
+ {
+ synchronized (_interpreters) {
+ _interpreters.put(className, interpreter);
+ }
+ }
+
+ /**
+ * Extract the .m files from the .jar plugin archive and write them as individual files
+ * in the plugin directory
+ */
+ private void installMatlabFunctions(PluginDescriptor descriptor, String ... functions) throws IOException
+ {
+ // Current plugin version
+ Version currentVersion = descriptor.getVersion();
+ if(currentVersion.isEmpty()) {
+ return; // Empty version correspond to the development version
+ }
+
+ // Known version for the plugin
+ Version knownVersion = getMatlabFunctionVersion(descriptor.getClassName());
+ if(!knownVersion.isEmpty() && currentVersion.equals(knownVersion)) {
+ return;
+ }
+
+ // Install the Matlab function files, remove the old one, and update the known version
+ Set<String> existingFunctions = getExistingMatlabFunctions(descriptor);
+ for(String fun : functions) {
+ existingFunctions.remove(fun);
+ extractMatlabFunction(descriptor, fun);
+ }
+ for(String fun : existingFunctions) {
+ deprecateMatlabFunction(descriptor, fun);
+ }
+ setMatlabFunctionVersion(descriptor.getClassName(), currentVersion);
+ }
+
+ /**
+ * Register a MatlabInterpreter plugin
+ */
+ private void registerInterpreter(PluginDescriptor descriptor)
+ throws IOException, InstantiationException, IllegalAccessException
+ {
+ // Append the plugin folder to the list of folders that should be append to
+ // the Matlab path
+ appendSourceFolder(descriptor);
+
+ // Save the instance of the plugin in the MatlabInterpreter index
+ MatlabInterpreter instance = (MatlabInterpreter)descriptor.getPluginClass().newInstance();
+ appendInterpreterInstance(descriptor.getClassName(), instance);
+
+ // Install the .m files and update the file read by the icy_init function
+ installMatlabFunctions(descriptor, instance.getFunctionNames());
+ }
+
+ @Override
+ public void init()
+ {
+ // Create the server
+ if(_instance!=null) {
+ throw new IllegalStateException(
+ "Trying to create a new instance of the Matlab communicator server while one is already running"
+ );
+ }
+ _instance = new MatlabCommunicatorServer(_sessions, _interpreters);
+
+ // Extract the Matlab function files
+ try {
+ installMatlabFunctions(getDescriptor(), "icy_init", "icy_command");
+ }
+ catch(IOException err) {
+ reportException(err);
+ }
+
+ // Register all the interpreters
+ clearInterpreterInstances();
+ clearSourceFolders();
+ for(PluginDescriptor descriptor : PluginLoader.getPlugins(MatlabInterpreter.class)) {
+ try {
+ registerInterpreter(descriptor);
+ }
+ catch(IOException err) {
+ reportException(err);
+ }
+ catch(RuntimeException err) {
+ throw err;
+ }
+ catch(Exception err) {
+ throw new RuntimeException(err);
+ }
+ }
+ }
+
+ @Override
+ public void run()
+ {
+ ThreadUtil.invokeLater(new Runnable()
+ {
+ @Override
+ public void run() {
+ showInstallMessage();
+ }
+ });
+
+ MatlabCommunicatorServer currentInstance = _instance;
+ if(currentInstance!=null) {
+ try {
+ currentInstance.run();
+ }
+ catch(IOException err) {
+ reportException(err);
+ }
+ }
+ }
+
+ @Override
+ public void stop()
+ {
+ if(_instance==null) {
+ throw new IllegalStateException(
+ "Trying to stop the Matlab communicator server while no instance is currently running"
+ );
+ }
+ try {
+ _instance.kill();
+ _instance = null;
+ }
+ catch(IOException err) {
+ reportException(err);
+ }
+ }
+
+ /**
+ * Display an error message
+ */
+ private static void reportException(final IOException err)
+ {
+ ThreadUtil.invokeLater(new Runnable()
+ {
+ @Override
+ public void run() {
+ System.err.println("Error encountered by the MatlabCommunicatorDeamon plugin:");
+ err.printStackTrace();
+ }
+ });
+ }
+}
diff --git a/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer.java b/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer.java
new file mode 100644
index 0000000000000000000000000000000000000000..a3c5b0affdf6bcdd97a86fa9a5abe7766d1dafac
--- /dev/null
+++ b/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer.java
@@ -0,0 +1,302 @@
+package plugins.ylemontag.matlabcommunicator;
+
+import icy.system.thread.ThreadUtil;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.net.InetSocketAddress;
+import java.net.ServerSocket;
+import java.net.Socket;
+import java.net.SocketAddress;
+import java.net.SocketException;
+import java.util.LinkedList;
+import java.util.Map;
+
+/**
+ *
+ * @author Yoann Le Montagner
+ *
+ * Set up a server waiting for commands issued by Matlab
+ */
+public class MatlabCommunicatorServer
+{
+ private Map<String, MatlabSession> _sessions;
+ private Map<String, MatlabInterpreter> _interpreters;
+ private int _port;
+ private boolean _killed;
+ private Object _runKillMutex;
+ private LinkedList<MatlabSocket> _sockets;
+ private ServerSocket _socketProvider;
+
+ /**
+ * Default constructor (use port 8732)
+ */
+ public MatlabCommunicatorServer(Map<String, MatlabSession> sessions,
+ Map<String, MatlabInterpreter> interpreters)
+ {
+ this(sessions, interpreters, 8732);
+ }
+
+ /**
+ * Constructor
+ */
+ public MatlabCommunicatorServer(Map<String, MatlabSession> sessions,
+ Map<String, MatlabInterpreter> interpreters, int port)
+ {
+ _sessions = sessions;
+ _interpreters = interpreters;
+ _port = port;
+ _killed = false;
+ _runKillMutex = new Object();
+ _sockets = new LinkedList<MatlabSocket>();
+ }
+
+ /**
+ * Enter the loop
+ */
+ public void run() throws IOException
+ {
+ // Create the socket if 'kill' has not been already called
+ synchronized (_runKillMutex)
+ {
+ if(_killed) {
+ return;
+ }
+ _socketProvider = new ServerSocket(_port);
+ }
+
+ // Wait for clients to connect
+ while(!_socketProvider.isClosed()) {
+ waitForConnection();
+ }
+ }
+
+ /**
+ * Stop the loop
+ */
+ public void kill() throws IOException
+ {
+ synchronized (_runKillMutex)
+ {
+ _killed = true;
+ if(_socketProvider==null || _socketProvider.isClosed()) {
+ return;
+ }
+ synchronized (_sockets) {
+ for(MatlabSocket socket : _sockets) {
+ socket.kill();
+ }
+ _sockets.clear();
+ }
+ _socketProvider.close();
+ }
+ }
+
+ /**
+ * Wait for a client to connect
+ */
+ private void waitForConnection() throws IOException
+ {
+ try {
+ final Socket socket = _socketProvider.accept();
+ SocketAddress remoteAddress = socket.getRemoteSocketAddress();
+ InetSocketAddress inetRemoteAddress = (InetSocketAddress)remoteAddress;
+ if(inetRemoteAddress==null || !inetRemoteAddress.getAddress().isLoopbackAddress()) {
+ throw new IOException("Unauthorized connection attempt from " + remoteAddress);
+ }
+ ThreadUtil.bgRun(new Runnable()
+ {
+ @Override
+ public void run() {
+ try {
+ MatlabSocket connection = new MatlabSocket(socket);
+ synchronized (_sockets) {
+ _sockets.push(connection);
+ }
+ connection.run();
+ }
+ catch(IOException err) {
+ reportException(err);
+ }
+ }
+ });
+ }
+ catch(SocketException se) {} // Exception received when the socket is closed
+ }
+
+ /**
+ * Encapsulate a socket
+ */
+ private class MatlabSocket
+ {
+ private Socket _socket;
+ private InputStream _in ;
+ private OutputStream _out ;
+
+ /**
+ * Constructor
+ */
+ public MatlabSocket(Socket socket) throws IOException
+ {
+ _socket = socket;
+ _in = _socket.getInputStream ();
+ _out = _socket.getOutputStream();
+ }
+
+ /**
+ * Receive the command, send the answer and close the connection
+ */
+ public void run() throws IOException
+ {
+ try {
+ String clientId = readLine();
+
+ // If the Matlab client haven't got an ID yet, create a new session,
+ // and return its parameters to the client
+ if(clientId.equals("?")) {
+ MatlabSession session = new MatlabSession();
+ putSession(session);
+ writeLine("ID");
+ writeLine(session.getClientId());
+ writeLine(session.getInput ().getAbsolutePath());
+ writeLine(session.getOutput().getAbsolutePath());
+ }
+
+ // Otherwise, try to retrieve the session object associated to the client
+ else {
+ MatlabSession session = getSession(clientId);
+ if(session==null) { // If the ID does not exist, return a 'Bad ID' error message
+ writeLine("Bad ID");
+ }
+
+ // Otherwise, try to retrieve the interpreter that is supposed to execute the command
+ else {
+ String className = readLine();
+ MatlabInterpreter interpreter = getInterpreter(className);
+ if(interpreter==null) // If the class name does not refer to a known Matlab interpreter object,
+ { // throw a 'Bad class name' error message
+ writeLine("Bad class name");
+ }
+
+ // Otherwise, execute the command
+ else {
+ String command = readLine();
+ try {
+ interpreter.execute(command, session);
+ writeLine("OK");
+ }
+ catch(MatlabCommandException err) {
+ writeLine("Fail");
+ writeLine(err.getMessage());
+ writeLine("Stack trace:");
+ for(StackTraceElement e : err.getStackTrace()) {
+ writeLine(" " + e.toString());
+ }
+ }
+ }
+ }
+ }
+ }
+
+ // Always close the socket at the end
+ finally {
+ writeLine("EOF");
+ _socket.close();
+ }
+ }
+
+ /**
+ * Stop the loop
+ */
+ public void kill() throws IOException
+ {
+ if(_socket.isClosed()) {
+ return;
+ }
+ _socket.close();
+ }
+
+ /**
+ * Read the given message (i.e. a text line) in the input stream
+ */
+ private String readLine() throws IOException
+ {
+ String retVal = "";
+ while(true) {
+ int rawChar = _in.read();
+ if(rawChar<0) {
+ throw new IOException("End of stream reached unexpectedly");
+ }
+ else if(rawChar==10 || rawChar==13) {
+ return retVal;
+ }
+ else {
+ retVal += (char)rawChar;
+ }
+ }
+ }
+
+ /**
+ * Send a message (i.e. a text line) through the output stream
+ */
+ private void writeLine(String message) throws IOException
+ {
+ int len = message.length();
+ byte[] buffer = new byte[len+1];
+ for(int k=0; k<len; ++k) {
+ buffer[k] = (byte)message.charAt(k);
+ }
+ buffer[len] = 10;
+ _out.write(buffer);
+ _out.flush();
+ }
+
+ /**
+ * Return the session object associated to the given client ID, or null if
+ * this client ID is unknown
+ */
+ private MatlabSession getSession(String clientId)
+ {
+ synchronized (_sessions) {
+ return _sessions.get(clientId);
+ }
+ }
+
+ /**
+ * Register the given session object
+ */
+ private void putSession(MatlabSession session)
+ {
+ synchronized (_sessions) {
+ _sessions.put(session.getClientId(), session);
+ }
+ }
+
+ /**
+ * Return the plugin instance corresponding to the given class name, or
+ * null if this class name has not been registered
+ */
+ private MatlabInterpreter getInterpreter(String className)
+ {
+ synchronized (_interpreters) {
+ return _interpreters.get(className);
+ }
+ }
+ }
+
+ /**
+ * Display an error message
+ */
+ private static void reportException(final IOException err)
+ {
+ ThreadUtil.invokeLater(new Runnable()
+ {
+ @Override
+ public void run() {
+ System.err.println("Error encountered while processing a Matlab command:");
+ err.printStackTrace();
+ }
+ });
+ }
+}
diff --git a/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabInterpreter.java b/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabInterpreter.java
new file mode 100644
index 0000000000000000000000000000000000000000..e7b91e7d9865480e6fe5a68741da1d873b466e06
--- /dev/null
+++ b/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabInterpreter.java
@@ -0,0 +1,21 @@
+package plugins.ylemontag.matlabcommunicator;
+
+/**
+ *
+ * @author Yoann Le Montagner
+ *
+ * Interface to implement to execute Matlab commands
+ */
+public interface MatlabInterpreter
+{
+ /**
+ * Return the names of the entry points to register, i.e. the names of all the
+ * Matlab functions that are provided by the plugin
+ */
+ public String[] getFunctionNames();
+
+ /**
+ * Execute a command
+ */
+ public void execute(String command, MatlabSession session) throws MatlabCommandException;
+}
diff --git a/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabSession.java b/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabSession.java
new file mode 100644
index 0000000000000000000000000000000000000000..e1ceb71d481fb3ddb4ec800cd92d97564eea2e1d
--- /dev/null
+++ b/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabSession.java
@@ -0,0 +1,94 @@
+package plugins.ylemontag.matlabcommunicator;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.UUID;
+
+/**
+ *
+ * @author Yoann Le Montagner
+ *
+ * Store the variables associated to a Matlab session (i.e. one Matlab client)
+ */
+public class MatlabSession
+{
+ private String _clientId;
+ private File _in ;
+ private File _out ;
+ private Map<String, Object> _objects ;
+
+ /**
+ * Constructor
+ */
+ public MatlabSession() throws IOException
+ {
+ _clientId = allocateClientId();
+ _in = allocateTemporaryFile();
+ _out = allocateTemporaryFile();
+ _objects = new HashMap<String, Object>();
+ }
+
+ /**
+ * Current client ID
+ */
+ public String getClientId()
+ {
+ return _clientId;
+ }
+
+ /**
+ * Current input file (communication from Matlab to the Icy server)
+ */
+ public File getInput()
+ {
+ return _in;
+ }
+
+ /**
+ * Current output file (communication from the Icy server to Matlab)
+ */
+ public File getOutput()
+ {
+ return _out;
+ }
+
+ /**
+ * Return the object with the given ID
+ */
+ public Object get(String name)
+ {
+ synchronized (_objects) {
+ return _objects.get(name);
+ }
+ }
+
+ /**
+ * Set the object with the given ID
+ */
+ public Object put(String name, Object obj)
+ {
+ synchronized (_objects) {
+ return _objects.put(name, obj);
+ }
+ }
+
+ /**
+ * Allocate a new client ID
+ */
+ private static String allocateClientId()
+ {
+ return UUID.randomUUID().toString();
+ }
+
+ /**
+ * Allocate a new temporary Matlab .mat file
+ */
+ private static File allocateTemporaryFile() throws IOException
+ {
+ File temporaryFile = File.createTempFile("icy_", ".mat");
+ temporaryFile.deleteOnExit();
+ return temporaryFile;
+ }
+}
diff --git a/src/main/resources/icon-Matlab-function-caller.png b/src/main/resources/icon-Matlab-function-caller.png
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diff --git a/src/main/resources/plugins/ylemontag/matlabcommunicator/icy_command.m b/src/main/resources/plugins/ylemontag/matlabcommunicator/icy_command.m
new file mode 100644
index 0000000000000000000000000000000000000000..d938ad6b177247db9cbfd069dcf78aa5b9520f85
--- /dev/null
+++ b/src/main/resources/plugins/ylemontag/matlabcommunicator/icy_command.m
@@ -0,0 +1,132 @@
+
+function args_out = icy_command(class_name, command, args_in)%#ok
+% args_out = icy_command(class_name, command, args_in)
+%
+% Low-level function to execute a command in Icy from Matlab.
+%
+% This function should not be used directly by final-users.
+
+% Sessions identifiers
+mlock;
+persistent client_ID;
+persistent path_in ;
+persistent path_out ;
+
+% Loop for session ID renewing
+remaining_attemps = 2;
+while(true)
+
+ % Get a session ID if necessary
+ if(~exist('client_ID', 'var') || isempty(client_ID))
+ msg_in = cell(1, 1);
+ msg_in{1} = '?';
+ msg_out = send_command(msg_in);
+ if(length(msg_out)~=4 || ~strcmp(msg_out{1}, 'ID'))
+ error('Unconsistent answer (expected: ID)');
+ end
+ client_ID = msg_out{2};
+ path_in = msg_out{3};
+ path_out = msg_out{4};
+ end
+ remaining_attemps = remaining_attemps - 1;
+
+ % Write the in file
+ if(~exist('args_in', 'var'))
+ args_in = struct();%#ok
+ end
+ save(path_in, '-struct', 'args_in');
+
+ % Execute the command
+ msg_in = cell(3, 1);
+ msg_in{1} = client_ID;
+ msg_in{2} = class_name;
+ msg_in{3} = command;
+ msg_out = send_command(msg_in);
+
+ % Interpret the result
+ if(length(msg_out)<1)
+ error('Unconsistent answer (no return code)');
+ end
+
+ % Code=='OK' => everything went well
+ if(strcmp(msg_out{1}, 'OK'))
+ args_out = load(path_out);
+ return;
+
+ % Code=='Fail' => error while executing the command
+ elseif(strcmp(msg_out{1}, 'Fail'))
+ error_message = '';
+ for p = 2:length(msg_out)
+ error_message = sprintf('%s\n %s', error_message, msg_out{p});
+ end
+ error('Error while executing the command "%s" with the plugin %s:%s', ...
+ command, class_name, error_message);
+
+ % Code=='Bad ID' => try to renew the client ID once
+ elseif(strcmp(msg_out{1}, 'Bad ID'))
+ if(remaining_attemps>0)
+ client_ID = [];
+ path_in = [];
+ path_out = [];
+ else
+ error('Invalid client ID: %s', client_ID);
+ end
+
+ % Code=='Bad class name' => the expected plugin interpreter does not exist on Icy
+ elseif(strcmp(msg_out{1}, 'Bad class name'))
+ error('The expected plugin (%s) is not installed on Icy', class_name);
+
+ % Unkown return code
+ else
+ error('Unconsistent answer (unknown return code: %s)', msg_out{1});
+ end
+end
+
+% Core function
+function msg_out = send_command(msg_in)
+
+ % Java stuff
+ import java.net.Socket
+ import java.io.*
+
+ % Establish the connection
+ socket = Socket('localhost', 8732);
+ out = socket.getOutputStream;
+ in = socket.getInputStream ;
+
+ % Send the list of strings
+ for k=1:length(msg_in)
+ buffer_in = uint8(sprintf('%s\n', msg_in{k}));
+ %fprintf('In: %s', buffer_in);
+ out.write(buffer_in);
+ end
+ out.flush();
+
+ % Wait for the answer and close the connection
+ msg_out = cell(0, 1);
+ msg_idx = 0;
+ buffer_out = zeros(1, 256);
+ buffer_idx = 0;
+ while(true)
+ current_char = in.read();
+ if(current_char<0)
+ error('End of stream reached unexpectedly');
+ elseif(current_char==10 || current_char==13)
+ current_answer = char(buffer_out(1:buffer_idx));
+ %fprintf('Out: %s\n', current_answer);
+ if(strcmp(current_answer, 'EOF'))
+ break;
+ end
+ msg_idx = msg_idx + 1;
+ msg_out{msg_idx} = current_answer;
+ buffer_out = zeros(1, 256);
+ buffer_idx = 0;
+ else
+ buffer_idx = buffer_idx + 1;
+ buffer_out(buffer_idx) = current_char;
+ end
+ end
+ socket.close();
+end
+
+end
diff --git a/src/main/resources/plugins/ylemontag/matlabcommunicator/icy_init.m b/src/main/resources/plugins/ylemontag/matlabcommunicator/icy_init.m
new file mode 100644
index 0000000000000000000000000000000000000000..7e98a3ab3a8d272f7222eba74d9c2bf9f3497d3b
--- /dev/null
+++ b/src/main/resources/plugins/ylemontag/matlabcommunicator/icy_init.m
@@ -0,0 +1,39 @@
+
+function icy_init()
+% icy_init()
+%
+% Append to the PATH Matlab environment variable all the folders that contain
+% Matlab functions in the Icy plugin directory.
+%
+% To initialize the functions provided by the Matlab<->Icy interaction plugins,
+% you have to execute the following commands each time you start Matlab:
+%
+% >> addpath('path/to/icy/plugins/ylemontag/matlabcommunicator');
+% >> icy_init();
+%
+% This operation can be done automatically using a startup.m file (please
+% consult the Matlab documentation for more details).
+
+% Current path
+myself = mfilename('fullpath');
+
+% Text file containing the list of source folders
+sep = find(myself=='/', 1, 'last');
+communicator_root = myself(1:sep);
+source_folder_file = [communicator_root 'source_folders.txt'];
+
+% Exit now if the source file does not exist
+if(~exist(source_folder_file, 'file'))
+ return;
+end
+
+% Read the file
+fid = fopen(source_folder_file, 'r');
+line = fgetl(fid);
+while(ischar(line))
+ if(exist(line, 'dir'))
+ addpath(line);
+ end
+ line = fgetl(fid);
+end
+fclose(fid);
diff --git a/src/main/resources/tooltip-Matlab-function-caller.png b/src/main/resources/tooltip-Matlab-function-caller.png
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