diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000000000000000000000000000000000000..bf0919262fbc7f5bb44035900379d0a110d3bd38 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,595 @@ +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". 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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. 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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. 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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..95cd6248db4a7b063fca36026123c8ec7841119b --- /dev/null +++ b/pom.xml @@ -0,0 +1,83 @@ +<?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-x-server</artifactId> + <version>3.2.0</version> + + <packaging>jar</packaging> + + <name>Matlab X Server</name> + <description>Use Icy as an image viewer from 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-communicator</artifactId> + <version>1.0.5</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/matlabxserver/MatlabXServerDeamon.java b/src/main/java/plugins/ylemontag/matlabxserver/MatlabXServerDeamon.java new file mode 100644 index 0000000000000000000000000000000000000000..1a5b305cab6000def6cd4d7d413ff8a537d9ef78 --- /dev/null +++ b/src/main/java/plugins/ylemontag/matlabxserver/MatlabXServerDeamon.java @@ -0,0 +1,568 @@ +package plugins.ylemontag.matlabxserver; + +import icy.gui.frame.progress.ProgressFrame; +import icy.image.lut.LUT; +import icy.main.Icy; +import icy.plugin.abstract_.Plugin; +import icy.roi.ROI; +import icy.roi.ROI2D; +import icy.roi.ROI2DLine; +import icy.roi.ROI2DRectangle; +import icy.sequence.Sequence; +import icy.system.thread.ThreadUtil; + +import java.awt.geom.Point2D; +import java.awt.geom.Rectangle2D; +import java.io.IOException; +import java.lang.ref.WeakReference; +import java.util.HashMap; +import java.util.LinkedList; +import java.util.List; +import java.util.Map; + +import plugins.ylemontag.matlabcommunicator.MatlabCommandException; +import plugins.ylemontag.matlabcommunicator.MatlabInterpreter; +import plugins.ylemontag.matlabcommunicator.MatlabSession; +import plugins.ylemontag.matlabio.ComplexMode; +import plugins.ylemontag.matlabio.DimensionMapping; +import plugins.ylemontag.matlabio.MatlabImporter; +import plugins.ylemontag.matlabio.gui.MatlabProgressFrame; +import plugins.ylemontag.matlabio.lib.Controller; +import plugins.ylemontag.matlabio.lib.MLArray; +import plugins.ylemontag.matlabio.lib.MLArrays; +import plugins.ylemontag.matlabio.lib.MLIOException; +import plugins.ylemontag.matlabio.lib.MLMeta; +import plugins.ylemontag.matlabio.lib.MLType; +import plugins.ylemontag.matlabio.lib.MatFileReader; +import plugins.ylemontag.matlabio.lib.MatFileWriter; + +/** + * + * @author Yoann Le Montagner + * + * Interpret and execute the display commands issued by Matlab + * + * @remark This class is suffixed by Deamon for historical reasons, although it + * is not a PluginDeamon anymore. + */ +public class MatlabXServerDeamon extends Plugin implements MatlabInterpreter +{ + @Override + public String[] getFunctionNames() + { + return new String[] { + "icy_figure" , + "icy_close" , + "icy_closeall" , + "icy_imshow" , + "icy_im3show" , + "icy_vidshow" , + "icy_vid3show" , + "icy_clearroi" , + "icy_line" , + "icy_rectangle", + "icy_gettitle" , + "icy_settitle" , + "icy_synclut" , + "icy_syncnav" , + "icy_mask" , //TODO: to be removed (the function is deprecated) + "icy_roimask" + }; + } + + @Override + public void execute(String command, MatlabSession session) throws MatlabCommandException + { + try { + MatFileReader reader = new MatFileReader(session.getInput()); + MatFileWriter writer = new MatFileWriter(session.getOutput(), false); + if (command.equals("figure" )) executeFigure (reader, writer, session); + else if(command.equals("close" )) executeClose (reader, writer, session); + else if(command.equals("closeall" )) executeCloseAll (reader, writer, session); + else if(command.equals("imshow" )) executeImShow (reader, writer, session); + else if(command.equals("im3show" )) executeIm3Show (reader, writer, session); + else if(command.equals("vidshow" )) executeVidShow (reader, writer, session); + else if(command.equals("vid3show" )) executeVid3Show (reader, writer, session); + else if(command.equals("clearroi" )) executeClearROI (reader, writer, session); + else if(command.equals("line" )) executeLine (reader, writer, session); + else if(command.equals("rectangle")) executeRectangle(reader, writer, session); + else if(command.equals("gettitle" )) executeGetTitle (reader, writer, session); + else if(command.equals("settitle" )) executeSetTitle (reader, writer, session); + else if(command.equals("synclut" )) executeSyncLut (reader, writer, session); + else if(command.equals("syncnav" )) executeSyncNav (reader, writer, session); + else if(command.equals("roimask" )) executeROIMask (reader, writer, session); + else { + throw new MatlabCommandException("Unknown command: " + command); + } + } + catch(IOException err) { + MatlabCommandException newErr = new MatlabCommandException(err); + newErr.setStackTrace(err.getStackTrace()); + throw newErr; + } + } + + /** + * Allocate a new viewer + */ + private void executeFigure(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + MLArray hFig = new MLArrays.Int32("h_fig", retrieveFigureIndex(session).allocateId()); + writer.putData(hFig); + } + + /** + * Close a figure + */ + private void executeClose(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + Sequence fig = retrieveFigureIndex(session).get(reader.getData("h_fig").getAsInt32()); + if(fig!=null) { + fig.close(); + } + } + + /** + * Close all the opened figures that belong to the current Matlab session + */ + private void executeCloseAll(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + List<Sequence> figs = retrieveFigureIndex(session).getAll(); + for(Sequence seq : figs) { + seq.close(); + } + } + + /** + * Display a 2D image + */ + private void executeImShow(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + DimensionMapping mapping = new DimensionMapping(); + mapping.setDimensionY(0); + mapping.setDimensionX(1); + mapping.setDimensionC(2); + mapping.setDimensionZ(3); + mapping.setDimensionT(4); + executeSomethingShow(reader, session, mapping); + } + + /** + * Display a 3D image + */ + private void executeIm3Show(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + DimensionMapping mapping = new DimensionMapping(); + mapping.setDimensionY(0); + mapping.setDimensionX(1); + mapping.setDimensionZ(2); + mapping.setDimensionC(3); + mapping.setDimensionT(4); + executeSomethingShow(reader, session, mapping); + } + + /** + * Display a 2D+T image + */ + private void executeVidShow(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + DimensionMapping mapping = new DimensionMapping(); + mapping.setDimensionY(0); + mapping.setDimensionX(1); + mapping.setDimensionT(2); + mapping.setDimensionC(3); + mapping.setDimensionZ(4); + executeSomethingShow(reader, session, mapping); + } + + /** + * Display a 3D+T image + */ + private void executeVid3Show(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + DimensionMapping mapping = new DimensionMapping(); + mapping.setDimensionY(0); + mapping.setDimensionX(1); + mapping.setDimensionZ(2); + mapping.setDimensionT(3); + mapping.setDimensionC(4); + executeSomethingShow(reader, session, mapping); + } + + /** + * Base function for imshow, im3show, vidshow and vid3show + */ + private void executeSomethingShow(MatFileReader reader, MatlabSession session, DimensionMapping mapping) + throws IOException + { + int hFig = reader.getData("h_fig").getAsInt32(); + Sequence fig = retrieveFigureIndex(session).get(hFig); + String title = reader.getData("title").getAsString(); + MatlabImporter importer = new MatlabImporter(reader); + Controller controller = new Controller(); + + // Create the sequence if the figure was not allocated before + if(fig==null) { + fig = new Sequence(); + retrieveFigureIndex(session).put(hFig, fig); + } + + // Import the data and display a progress frame so that the user can interrupt the operation + ProgressFrame progressFrame = new MatlabProgressFrame( + "Displaying " + title + "...", controller + ); + try { + fig.setName(title); + importer.getSequence("data", mapping, ComplexMode.BOTH, fig, controller); + addSequenceIfNoViewer(fig); + } + catch(Controller.CanceledByUser e) {} + + // Don't forget to close the progress frame + finally { + progressFrame.close(); + } + } + + /** + * Show the given sequence if it has no viewer yet + */ + private static void addSequenceIfNoViewer(final Sequence seq) + { + ThreadUtil.invokeLater(new Runnable() + { + public void run() { + if(seq.getViewers().isEmpty()) { + Icy.getMainInterface().addSequence(seq); + } + else { + seq.getFirstViewer().toFront(); + } + } + }); + } + + /** + * Remove a ROI from the given figure + */ + private void executeClearROI(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + Sequence fig = retrieveFigureIndex(session).get(reader.getData("h_fig").getAsInt32()); + int hRoi = reader.getData("h_roi").getAsInt32(); + + // Stop if the figure does not exist + if(fig==null) { + return; + } + + // Remove the ROI if it exists + ROI target = null; + for(ROI roi : fig.getROIs()) { + if(roi.getId()==hRoi) { + target = roi; + break; + } + } + if(target!=null) { + fig.removeROI(target); + } + } + + /** + * Create a line ROI on the figure, and return its ID + */ + private void executeLine(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException, MatlabCommandException + { + Sequence fig = retrieveFigureIndex(session).get(reader.getData("h_fig").getAsInt32()); + double[] data = extractRoiCoordinates(reader, 4); + if(fig==null) { + return; + } + ROI2DLine roi = new ROI2DLine(new Point2D.Double(data[0], data[1]), new Point2D.Double(data[2], data[3])); + fig.addROI(roi); + saveRoiId(writer, roi); + } + + /** + * Create a rectangle ROI on the figure, and return its ID + */ + private void executeRectangle(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException, MatlabCommandException + { + Sequence fig = retrieveFigureIndex(session).get(reader.getData("h_fig").getAsInt32()); + double[] data = extractRoiCoordinates(reader, 4); + if(fig==null) { + return; + } + ROI2DRectangle roi = new ROI2DRectangle(); + roi.setRectangle(new Rectangle2D.Double(data[0], data[1], data[2], data[3])); + fig.addROI(roi); + saveRoiId(writer, roi); + } + + /** + * Extract the field named 'coordinates' from the given .mat file reader, and + * cast it as an double array with the given expected size + */ + private double[] extractRoiCoordinates(MatFileReader reader, int expectedSize) + throws IOException, MatlabCommandException + { + MLMeta meta = reader.getMeta("coordinates"); + if(meta==null || meta.getType()!=MLType.DOUBLE || meta.getSize()!=expectedSize || meta.getIsComplex()) { + throw new MatlabCommandException("Invalid ROI coordinates"); + } + return ((MLArrays.Double)reader.getData("coordinates")).getReal(); + } + + /** + * Save the index of the given ROI to the output file + */ + private void saveRoiId(MatFileWriter writer, ROI roi) throws IOException + { + MLArray h_roi = new MLArrays.Int32("h_roi", roi.getId()); + writer.putData(h_roi); + } + + /** + * Return the title of the given figure + */ + private void executeGetTitle(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + Sequence fig = retrieveFigureIndex(session).get(reader.getData("h_fig").getAsInt32()); + MLArray title = new MLArrays.Char("title", fig==null ? "" : fig.getName()); + writer.putData(title); + } + + /** + * Change the title of a figure + */ + private void executeSetTitle(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + Sequence fig = retrieveFigureIndex(session).get(reader.getData("h_fig").getAsInt32()); + String title = reader.getData("title").getAsString(); + if(fig!=null) { + fig.setName(title); + } + } + + /** + * Synchronize the LUT of several figures + */ + private void executeSyncLut(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + FigureIndex index = retrieveFigureIndex(session); + final Sequence master = index.get(reader.getData("h_master").getAsInt32()); + final Sequence[] slaves = index.get(reader.getData("h_slaves").getAsInt32Array()); + ThreadUtil.invokeLater(new Runnable() + { + @Override + public void run() { + if(master==null || master.getFirstViewer()==null) { + return; + } + LUT lut = master.getFirstViewer().getLut(); + for(Sequence slave : slaves) { + if(slave==null || slave.getFirstViewer()==null) { + continue; + } + slave.getFirstViewer().getLut().setScalers(lut); + } + } + }); + } + + /** + * Synchronize the navigation of several figures + */ + private void executeSyncNav(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + FigureIndex index = retrieveFigureIndex(session); + final Sequence master = index.get(reader.getData("h_master").getAsInt32()); + final Sequence[] slaves = index.get(reader.getData("h_slaves").getAsInt32Array()); + ThreadUtil.invokeLater(new Runnable() + { + @Override + public void run() { + if(master==null || master.getFirstViewer()==null) { + return; + } + for(Sequence slave : slaves) { + if(slave==null || slave.getFirstViewer()==null) { + continue; + } + master.getFirstViewer().getCanvas().setSyncId(0); + slave .getFirstViewer().getCanvas().setSyncId(1); + master.getFirstViewer().getCanvas().setSyncId(1); + } + } + }); + } + + /** + * Let the user draw a ROI on the given sequence, and return the corresponding mask + */ + private void executeROIMask(MatFileReader reader, MatFileWriter writer, MatlabSession session) + throws IOException + { + Sequence fig = retrieveFigureIndex(session).get(reader.getData("h_fig").getAsInt32()); + if(fig==null) { + return; + } + addSequenceIfNoViewer(fig); + String label = reader.getData("label").getAsString(); + ROISelectorOverlay overlay = new ROISelectorOverlay(fig, label); + ROISelectorFuture future = new ROISelectorFuture(overlay); + ROI roi = future.getSelectedROI(); + MLArray mask = convertToMatlabBooleanMask("mask", fig, roi); + MLArray hRoi = new MLArrays.Int32("h_roi", roi==null ? 0 : roi.getId()); + writer.putData(mask); + writer.putData(hRoi); + } + + /** + * Convert a pair ROI+sequence into a Matlab boolean mask + */ + private static MLArrays.Logical convertToMatlabBooleanMask(String name, Sequence seq, ROI roi) + throws MLIOException + { + // Return an empty array if no ROI is given + if(roi==null) { + return new MLArrays.Logical(name, new boolean[0]); + } + + // Extract the boolean mask (in Icy's format) + boolean[] mask = ((ROI2D)roi).getBooleanMask(seq.getBounds()); + + // Convert the Icy boolean mask into a Matlab boolean mask (i.e. essentially + // swap the X and Y dimensions) + int sizeX = seq.getSizeX(); + int sizeY = seq.getSizeY(); + MLArrays.Logical retVal = new MLArrays.Logical(new MLMeta(MLType.LOGICAL, name, + new int[] {sizeY, sizeX}, false)); + int offsetIcy = 0; + for(int y=0; y<sizeY; ++y) { + for(int x=0; x<sizeX; ++x) { + retVal.get()[x*sizeY + y] = mask[offsetIcy]; + ++offsetIcy; + } + } + return retVal; + } + + /** + * Retrieve the data structure that holds the existing figures + */ + private static FigureIndex retrieveFigureIndex(MatlabSession session) + { + Object retVal = session.get("xserver_figures"); + if(retVal==null) { + FigureIndex newObject = new FigureIndex(); + session.put("xserver_figures", newObject); + return newObject; + } + else { + return (FigureIndex)retVal; + } + } + + /** + * Object used to store map the figure IDs (integers) to the sequences + */ + private static class FigureIndex + { + private int _suggestedId; + private Map<Integer, WeakReference<Sequence>> _data; + + /** + * Constructor + */ + public FigureIndex() + { + _suggestedId = 1; + _data = new HashMap<Integer, WeakReference<Sequence>>(); + } + + /** + * Allocate a new figure ID + */ + public int allocateId() + { + while(_data.containsKey(_suggestedId)) { + ++_suggestedId; + } + _data.put(_suggestedId, null); + return _suggestedId; + } + + /** + * Return all the existing figures + * @remarks No null object in the returned list + */ + public List<Sequence> getAll() + { + List<Sequence> retVal = new LinkedList<Sequence>(); + for(WeakReference<Sequence> ref : _data.values()) { + if(ref==null) { + continue; + } + Sequence seq = ref.get(); + if(seq==null) { + continue; + } + retVal.add(seq); + } + return retVal; + } + + /** + * Get the sequence corresponding to the given figure ID + * @remarks The returned object may be null in the figure ID is not valid, + * or if the viewer corresponding to the figure has been closed + * by the user. + */ + public Sequence get(int hFig) + { + if(_data.containsKey(hFig)) { + WeakReference<Sequence> ref = _data.get(hFig); + return ref==null ? null : ref.get(); + } + else { + _data.put(hFig, null); + return null; + } + } + + /** + * Return the sequences corresponding to the given figure IDs + */ + public Sequence[] get(int[] hFigs) + { + Sequence[] retVal = new Sequence[hFigs.length]; + for(int k=0; k<hFigs.length; ++k) { + retVal[k] = get(hFigs[k]); + } + return retVal; + } + + /** + * Define the sequence corresponding to the given figure ID + */ + public void put(int hFig, Sequence seq) + { + _data.put(hFig, seq==null ? null : new WeakReference<Sequence>(seq)); + } + } +} diff --git a/src/main/java/plugins/ylemontag/matlabxserver/ROISelectorFuture.java b/src/main/java/plugins/ylemontag/matlabxserver/ROISelectorFuture.java new file mode 100644 index 0000000000000000000000000000000000000000..deb34b98601ad288f462b57b8cac78aa3a8e69d8 --- /dev/null +++ b/src/main/java/plugins/ylemontag/matlabxserver/ROISelectorFuture.java @@ -0,0 +1,82 @@ +package plugins.ylemontag.matlabxserver; + +import icy.roi.ROI; + +import java.util.concurrent.locks.Condition; +import java.util.concurrent.locks.ReentrantLock; + +/** + * + * @author Yoann Le Montagner + * + * Wrap a mutex and a condition, to make + */ +public class ROISelectorFuture +{ + ReentrantLock _lock ; + Condition _condition ; + boolean _isReady ; + ROI _selectedRoi; + + /** + * Constructor + */ + public ROISelectorFuture(ROISelectorOverlay overlay) + { + _lock = new ReentrantLock(); + _condition = _lock.newCondition(); + _isReady = false; + overlay.addListener(new ROISelectorOverlay.Listener() + { + @Override + public void onOkClicked(ROI selectedRoi) + { + onButtonClicked(selectedRoi); + } + + @Override + public void onCancelClicked() + { + onButtonClicked(null); + } + }); + } + + /** + * Make the current thread wait until the user clicks one of the button drawn + * by the ROI selector painter, and return the selected ROI if any + */ + public ROI getSelectedROI() + { + _lock.lock(); + try { + while(!_isReady) { + try { + _condition.await(); + } + catch (InterruptedException e) {} + } + return _selectedRoi; + } + finally { + _lock.unlock(); + } + } + + /** + * Action performed when the user clicks on one of the button drawn by + * the ROI selector painter + */ + private void onButtonClicked(ROI selectedRoi) + { + _lock.lock(); + try { + _isReady = true; + _selectedRoi = selectedRoi; + _condition.signalAll(); + } + finally { + _lock.unlock(); + } + } +} diff --git a/src/main/java/plugins/ylemontag/matlabxserver/ROISelectorOverlay.java b/src/main/java/plugins/ylemontag/matlabxserver/ROISelectorOverlay.java new file mode 100644 index 0000000000000000000000000000000000000000..6bf679634dc331a86505b6e29dc1c4afaf26d763 --- /dev/null +++ b/src/main/java/plugins/ylemontag/matlabxserver/ROISelectorOverlay.java @@ -0,0 +1,265 @@ +package plugins.ylemontag.matlabxserver; + +import icy.canvas.Canvas2D; +import icy.canvas.IcyCanvas; +import icy.painter.Overlay; +import icy.roi.ROI; +import icy.sequence.Sequence; +import icy.sequence.SequenceAdapter; +import icy.util.GraphicsUtil; + +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Graphics2D; +import java.awt.event.MouseEvent; +import java.awt.geom.Point2D; +import java.util.LinkedList; +import java.util.List; + +/** + * + * @author Yoann Le Montagner + * + * Painter proposing to create a new ROI on the sequence or to select one + */ +public class ROISelectorOverlay extends Overlay +{ + /** + * Interface to implement to listen events sent by the painter + */ + public static interface Listener + { + /** + * Click on the validation button + */ + public void onOkClicked(ROI selectedRoi); + + /** + * Click on the cancel button + */ + public void onCancelClicked(); + } + + private static final int NORMAL = 0; + private static final int HOVER = 1; + private static final int DISABLED = 2; + + private Sequence _sequence; + private List<Listener> _listeners; + private String _labelInfo; + private String _labelOk ; + private String _labelCl ; + private Color[] _bg; + private Color[] _fg; + private boolean _hintPositionComputed; + private int _xInfo; + private int _xOk ; + private int _xCl ; + private int _yInfo; + private int _yOk ; + private int _yCl ; + private Dimension _sizeInfo; + private Dimension _sizeOk ; + private Dimension _sizeCl ; + private boolean _hoverOk; + private boolean _hoverCl; + + /** + * Constructor with default text label + */ + public ROISelectorOverlay(Sequence sequence) + { + this(sequence, ""); + } + + /** + * Constructor + */ + public ROISelectorOverlay(Sequence sequence, String instruction) + { + super("Matlab ROI selector", OverlayPriority.TEXT_NORMAL); + if(sequence==null) { + throw new IllegalArgumentException("Argument 'sequence' cannot be null."); + } + _listeners = new LinkedList<Listener>(); + _labelInfo = instruction.isEmpty() ? "Select an existing ROI or create a new one." : instruction; + _labelOk = "Validate"; + _labelCl = "Cancel"; + _bg = new Color[] { new Color(0,128,255), new Color(255,64,0), Color.GRAY }; + _fg = new Color[] { Color.WHITE , Color.WHITE , Color.BLACK}; + _hoverOk = false; + _hoverCl = false; + _hintPositionComputed = false; + _sequence = sequence; + _sequence.addPainter(this); + _sequence.addListener(new SequenceAdapter() + { + @Override + public void sequenceClosed(Sequence sequence) + { + fireCancel(); + } + }); + } + + /** + * Add a new listener + */ + public void addListener(Listener l) + { + _listeners.add(l); + } + + /** + * Remove a listener + */ + public void removeListener(Listener l) + { + _listeners.remove(l); + } + + @Override + public void paint(Graphics2D g0, Sequence sequence, IcyCanvas canvas) + { + if(g0==null) return; + Graphics2D g = null; + try { + g = (Graphics2D)g0.create(); + + // Use the viewer coordinates + g.transform(((Canvas2D)canvas).getInverseTransform()); + + // Compute the position of the hints + ensureHintPositionComputed(g); + + // Draw the hints + int stateOk = _sequence.getSelectedROI()==null ? DISABLED : (_hoverOk ? HOVER : NORMAL); + int stateCl = _hoverCl ? HOVER : NORMAL; + GraphicsUtil.drawHint(g, _labelInfo, _xInfo, _yInfo, _bg[NORMAL ], _fg[NORMAL ]); + GraphicsUtil.drawHint(g, _labelOk , _xOk , _yOk , _bg[stateOk], _fg[stateOk]); + GraphicsUtil.drawHint(g, _labelCl , _xCl , _yCl , _bg[stateCl], _fg[stateCl]); + } + + // Release the graphics object + finally { + if(g!=null) { + g.dispose(); + } + } + } + + @Override + public void mousePressed(MouseEvent e, Point2D imagePoint, IcyCanvas canvas) + { + if(e.isConsumed()) { + return; + } + if(_hoverOk || _hoverCl) { // Two different mouse events are generated when + e.consume(); // clicking on the mouse: mousePressed and + } // mouseClick. These two events must be consumed + } // together to avoid strange behaviors. + + @Override + public void mouseClick(MouseEvent e, Point2D imagePoint, IcyCanvas canvas) + { + if(e.isConsumed()) { + return; + } + if(_hoverOk) { + e.consume(); + fireOk(); + } + else if(_hoverCl) { + e.consume(); + fireCancel(); + } + } + + @Override + public void mouseMove(MouseEvent e, Point2D imagePoint, IcyCanvas canvas) + { + if(refreshHover(e)) { + _sequence.painterChanged(this); + } + } + + /** + * Computes the position where the various hints should be displayed + */ + private void ensureHintPositionComputed(Graphics2D g) + { + if(_hintPositionComputed) { + return; + } + + // Position and size of the label + _xInfo = 3; + _yInfo = 3; + _sizeInfo = GraphicsUtil.getHintSize(g, _labelInfo); + + // Position and size of the cancel button + _xCl = 3; + _yCl = 6 + _sizeInfo.height; + _sizeCl = GraphicsUtil.getHintSize(g, _labelCl); + + // Position of the validation button + _xOk = 6 + _sizeCl.width; + _yOk = _yCl; + _sizeOk = GraphicsUtil.getHintSize(g, _labelOk); + + // Done! + _hintPositionComputed = true; + } + + /** + * Refresh the hover flags (that indicate whether the mouse cursor is over + * the OK/cancel buttons or not) + * @return true if at least one the two flags has changed + */ + private boolean refreshHover(MouseEvent e) + { + // The size of the hints must have been computed before + if(!_hintPositionComputed) { + return false; + } + + // Old values + boolean oldHoverOk = _hoverOk; + boolean oldHoverCl = _hoverCl; + + // Position of the cursor, in viewer coordinates + int x = e.getX(); + int y = e.getY(); + + // Refresh the flags + _hoverOk = (x>=_xOk) && (y>=_yOk) && (x<_xOk+_sizeOk.width) && (y<_yOk+_sizeOk.height); + _hoverCl = (x>=_xCl) && (y>=_yCl) && (x<_xCl+_sizeCl.width) && (y<_yCl+_sizeCl.height); + return oldHoverOk!=_hoverOk || oldHoverCl!=_hoverCl; + } + + /** + * Fire the listener, cancel event + */ + private void fireCancel() + { + _sequence.removePainter(this); + for(Listener l : _listeners) { + l.onCancelClicked(); + } + } + + /** + * Fire the listener, OK event + */ + private void fireOk() + { + ROI roi = _sequence.getSelectedROI(); + if(roi==null) { + return; + } + _sequence.removePainter(this); + for(Listener l : _listeners) { + l.onOkClicked(roi); + } + } +} diff --git a/src/main/resources/icon-Matlab-function-caller.png b/src/main/resources/icon-Matlab-function-caller.png new file mode 100644 index 0000000000000000000000000000000000000000..d66688871bd6a31c7e2aaaf1fe366264097df00d Binary files /dev/null and b/src/main/resources/icon-Matlab-function-caller.png differ diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_clearroi.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_clearroi.m new file mode 100644 index 0000000000000000000000000000000000000000..21bab24ba42817fcdfe911120ba5bc582a57b6c7 --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_clearroi.m @@ -0,0 +1,10 @@ + +function icy_clearroi(h_fig, h_roi) +% icy_clearroi(h_fig, h_roi) +% +% Clear the ROI that corresponds to the handle 'h_roi' from the figure +% identified by 'h_fig'. + +args_in.h_fig = int32(h_fig); +args_in.h_roi = int32(h_roi); +icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'clearroi', args_in); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_close.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_close.m new file mode 100644 index 0000000000000000000000000000000000000000..cca5dea1005d4761aa57a2350e295088263d2384 --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_close.m @@ -0,0 +1,8 @@ + +function icy_close(h_fig) +% icy_close(h_fig) +% +% Close all the viewers that corresponds to the handle 'h_fig'. + +args_in.h_fig = int32(h_fig); +icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'close', args_in); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_closeall.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_closeall.m new file mode 100644 index 0000000000000000000000000000000000000000..b2782cf644fa5b506853ecde790213241ae99c9d --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_closeall.m @@ -0,0 +1,23 @@ + +function icy_closeall(close_matlab_figures_too) +% icy_closeall() +% icy_closeall(close_matlab_figures_too) +% +% Close all the viewers that belong to the current session. +% +% The usual Matlab figures can also be closed by the command, by setting the +% optional 'close_matlab_figures_too' flag to true. This is the default behavior +% if the flag is not specified. + +% Optional parameter +if(~exist('close_matlab_figures_too', 'var')) + close_matlab_figures_too = true; +end + +% Execute the command +icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'closeall'); + +% Close the matlab figures +if(close_matlab_figures_too) + close all; +end diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_figure.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_figure.m new file mode 100644 index 0000000000000000000000000000000000000000..ea14ebee9ba7d8fac979fc33c4eacb67dfec5485 --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_figure.m @@ -0,0 +1,8 @@ + +function h_fig = icy_figure() +% h_fig = icy_figure() +% +% Allocate a new viewer in Icy, and return its handle. + +args_out = icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'figure'); +h_fig = double(args_out.h_fig); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_gettitle.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_gettitle.m new file mode 100644 index 0000000000000000000000000000000000000000..8b666b90936f4f6d2d10d1b492fac41fda1112d8 --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_gettitle.m @@ -0,0 +1,9 @@ + +function title = icy_gettitle(h_fig) +% title = icy_gettitle(h_fig) +% +% Return the title of the figure corresponding to the handle 'h_fig'. + +args_in.h_fig = int32(h_fig); +args_out = icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'gettitle', args_in); +title = args_out.title; diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_im3show.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_im3show.m new file mode 100644 index 0000000000000000000000000000000000000000..6c0d5a9d6e91aa6e93990235a1d4a4bc47b033f5 --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_im3show.m @@ -0,0 +1,43 @@ + +function h_fig = icy_im3show(h_fig, data, title) +% h_fig = icy_im3show(data) +% h_fig = icy_im3show(data, title) +% h_fig = icy_im3show(h_fig, data) +% h_fig = icy_im3show(h_fig, data, title) +% +% Display the 3D image 'data' in Icy, and return the handle of the corresponding +% figure. +% +% If the 'h_fig' argument is provided, the corresponding figure is used; +% otherwise, a new figure is created. If the 'title' argument is provided, +% the function will also change the title of the figure, otherwise it is let +% unchanged. + +% Allocate a new figure if necessary +if(~exist('title', 'var') && exist('data', 'var') && ischar(data)) + title = data; + data = h_fig; + h_fig = icy_figure(); +elseif(~exist('data', 'var')) + data = h_fig; + h_fig = icy_figure(); +end + +% Default title +persistent counter; +if(isempty(counter)) + counter = 0; +end +if(~exist('title', 'var')) + title = icy_gettitle(h_fig); + if(isempty(title)) + counter = counter + 1; + title = sprintf('Image 3D %d', counter); + end +end + +% Execute the command +args_in.h_fig = int32(h_fig); +args_in.title = title; +args_in.data = data; +icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'im3show', args_in); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_imshow.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_imshow.m new file mode 100644 index 0000000000000000000000000000000000000000..9417ea0256261316bf4abeaa8a39fcd4f4d039e0 --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_imshow.m @@ -0,0 +1,43 @@ + +function h_fig = icy_imshow(h_fig, data, title) +% h_fig = icy_imshow(data) +% h_fig = icy_imshow(data, title) +% h_fig = icy_imshow(h_fig, data) +% h_fig = icy_imshow(h_fig, data, title) +% +% Display the image 'data' in Icy, and return the handle of the corresponding +% figure. +% +% If the 'h_fig' argument is provided, the corresponding figure is used; +% otherwise, a new figure is created. If the 'title' argument is provided, +% the function will also change the title of the figure, otherwise it is let +% unchanged. + +% Allocate a new figure if necessary +if(~exist('title', 'var') && exist('data', 'var') && ischar(data)) + title = data; + data = h_fig; + h_fig = icy_figure(); +elseif(~exist('data', 'var')) + data = h_fig; + h_fig = icy_figure(); +end + +% Default title +persistent counter; +if(isempty(counter)) + counter = 0; +end +if(~exist('title', 'var')) + title = icy_gettitle(h_fig); + if(isempty(title)) + counter = counter + 1; + title = sprintf('Image %d', counter); + end +end + +% Execute the command +args_in.h_fig = int32(h_fig); +args_in.title = title; +args_in.data = data; +icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'imshow', args_in); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_line.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_line.m new file mode 100644 index 0000000000000000000000000000000000000000..8bd996b63de2d1795a15b2bab26a70b9210e396f --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_line.m @@ -0,0 +1,27 @@ + +function h_roi = icy_line(h_fig, x1, y1, x2, y2) +% h_roi = icy_line(h_fig, x1, y1, x2, y2) +% h_roi = icy_line(h_fig, [x1, y1, x2, y2]) +% +% Create a linear ROI in the figure identified by 'h_fig', and return a +% handle that can be used to identified this ROI. +% +% The line will be created between the points (x1,y1) and (x2,y2), where 'x1' +% and 'x2' represent horizontal coordinates, and 'y1' and 'y2' vertical +% coordinates. Be careful when setting these values, as Icy and Matlab does not +% use the same convention to identify the top-left coordinate of an image: +% (1,1) in Matlab, but (0,0) in Icy. + +% Compute the coordinates +if(numel(x1)==4) + coordinates = x1; +else + coordinates = [x1, y1, x2, y2]; +end +coordinates = double(coordinates); + +% Execute the command +args_in.h_fig = int32(h_fig); +args_in.coordinates = coordinates; +args_out = icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'line', args_in); +h_roi = double(args_out.h_roi); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_mask.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_mask.m new file mode 100644 index 0000000000000000000000000000000000000000..3eae04e7dadc166301d1ad9ba89cc24d6d2e496d --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_mask.m @@ -0,0 +1,8 @@ + +function [mask, h_roi] = icy_mask(h_fig) +% +% The function 'icy_mask' is deprecated: use 'icy_roimask' instead. +% + +fprintf('The function ''icy_mask'' is deprecated: use ''icy_roimask'' instead.\n'); +[mask, h_roi] = icy_roimask(h_fig); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_rectangle.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_rectangle.m new file mode 100644 index 0000000000000000000000000000000000000000..1dde856b1722df5b7179e835cf4622f39afad064 --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_rectangle.m @@ -0,0 +1,27 @@ + +function h_roi = icy_rectangle(h_fig, x0, y0, width, height) +% h_roi = icy_rectangle(h_fig, x0, y0, width, height) +% h_roi = icy_rectangle(h_fig, [x0, y0, width, height]) +% +% Create a rectangular ROI in the figure identified by 'h_fig', and return a +% handle that can be used to identified this ROI. +% +% The variable 'x0' and 'y0' specify the position of the top-left corner of the +% ROI, while 'width' and 'height' determine respectively the horizontal and +% vertical dimensions of the rectangle. Be careful when setting 'x0' and 'y0', +% as Icy and Matlab does not use the same convention to identify the top-left +% coordinate of an image: (1,1) in Matlab, but (0,0) in Icy. + +% Compute the coordinates +if(numel(x0)==4) + coordinates = x0; +else + coordinates = [x0, y0, width, height]; +end +coordinates = double(coordinates); + +% Execute the command +args_in.h_fig = int32(h_fig); +args_in.coordinates = coordinates; +args_out = icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'rectangle', args_in); +h_roi = double(args_out.h_roi); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_roimask.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_roimask.m new file mode 100644 index 0000000000000000000000000000000000000000..61cf41cc43be5300207409be1ed216fae3a9cde8 --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_roimask.m @@ -0,0 +1,22 @@ + +function [mask, h_roi] = icy_roimask(h_fig, label) +% [mask, h_roi] = icy_roimask(h_fig) +% [mask, h_roi] = icy_roimask(h_fig, label) +% +% Ask the user to select an existing ROI or to create a new one on the figure +% identified by 'h_fig', and return the corresponding 2D boolean mask, and also +% a handle that can be used to identified the selected ROI. +% +% This function provides a similar feature than the Matlab built-in 'roipoly' +% function. + +% Optional label argument +if(~exist('label', 'var')) + label = ''; +end + +args_in.h_fig = int32(h_fig); +args_in.label = char(label); +args_out = icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'roimask', args_in); +mask = args_out.mask; +h_roi = args_out.h_roi; diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_settitle.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_settitle.m new file mode 100644 index 0000000000000000000000000000000000000000..39d93d2875ef2c0f447ea64e042fd288aeebe20e --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_settitle.m @@ -0,0 +1,9 @@ + +function icy_settitle(h_fig, title) +% icy_settitle(h_fig, title) +% +% Change the title of the figure corresponding to the handle 'h_fig' + +args_in.h_fig = int32(h_fig); +args_in.title = title; +icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'settitle', args_in); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_synclut.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_synclut.m new file mode 100644 index 0000000000000000000000000000000000000000..4b494a25c3e56cc7cf6b4038e0bba88ed57118f4 --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_synclut.m @@ -0,0 +1,20 @@ + +function icy_synclut(h_master, varargin) +% icy_synclut(h_master, h_slave) +% icy_synclut(h_master, h_slave1, h_slave2) +% icy_synclut(h_master, h_slave1, h_slave2, ...) +% +% Copy the look-up table (i.e. the color map) of the figure corresponding to +% 'h_master' to the ones corresponding to 'h_slave1', 'h_slave2', etc... + +% Extract the list of slave figures to synchronize +nb_slaves = length(varargin); +h_slaves = zeros(nb_slaves, 1); +for k=1:length(varargin) + h_slaves(k) = varargin{k}; +end + +% Execute the command +args_in.h_master = int32(h_master); +args_in.h_slaves = int32(h_slaves); +icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'synclut', args_in); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_syncnav.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_syncnav.m new file mode 100644 index 0000000000000000000000000000000000000000..d55eb56dabc46f4893be8c2cf4921a29c3f1498d --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_syncnav.m @@ -0,0 +1,20 @@ + +function icy_syncnav(h_master, varargin) +% icy_syncnav(h_master, h_slave) +% icy_syncnav(h_master, h_slave1, h_slave2) +% icy_syncnav(h_master, h_slave1, h_slave2, ...) +% +% Synchronize the navigation in the figures corresponding to 'h_master', +% 'h_slave1', 'h_slave2', etc... + +% Extract the list of slave figures to synchronize +nb_slaves = length(varargin); +h_slaves = zeros(nb_slaves, 1); +for k=1:length(varargin) + h_slaves(k) = varargin{k}; +end + +% Execute the command +args_in.h_master = int32(h_master); +args_in.h_slaves = int32(h_slaves); +icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'syncnav', args_in); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_vid3show.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_vid3show.m new file mode 100644 index 0000000000000000000000000000000000000000..c5538177d42f6f413b4ea5a17d19e7c6a231f7b1 --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_vid3show.m @@ -0,0 +1,43 @@ + +function h_fig = icy_vid3show(h_fig, data, title) +% h_fig = icy_vid3show(data) +% h_fig = icy_vid3show(data, title) +% h_fig = icy_vid3show(h_fig, data) +% h_fig = icy_vid3show(h_fig, data, title) +% +% Display the 3D+T image 'data' in Icy, and return the handle of the +% corresponding figure. +% +% If the 'h_fig' argument is provided, the corresponding figure is used; +% otherwise, a new figure is created. If the 'title' argument is provided, +% the function will also change the title of the figure, otherwise it is let +% unchanged. + +% Allocate a new figure if necessary +if(~exist('title', 'var') && exist('data', 'var') && ischar(data)) + title = data; + data = h_fig; + h_fig = icy_figure(); +elseif(~exist('data', 'var')) + data = h_fig; + h_fig = icy_figure(); +end + +% Default title +persistent counter; +if(isempty(counter)) + counter = 0; +end +if(~exist('title', 'var')) + title = icy_gettitle(h_fig); + if(isempty(title)) + counter = counter + 1; + title = sprintf('Video 3D %d', counter); + end +end + +% Execute the command +args_in.h_fig = int32(h_fig); +args_in.title = title; +args_in.data = data; +icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'vid3show', args_in); diff --git a/src/main/resources/plugins/ylemontag/matlabxserver/icy_vidshow.m b/src/main/resources/plugins/ylemontag/matlabxserver/icy_vidshow.m new file mode 100644 index 0000000000000000000000000000000000000000..83582a0ec5e7a4419f1c73a27c6b5e4e6a722c72 --- /dev/null +++ b/src/main/resources/plugins/ylemontag/matlabxserver/icy_vidshow.m @@ -0,0 +1,43 @@ + +function h_fig = icy_vidshow(h_fig, data, title) +% h_fig = icy_vidshow(data) +% h_fig = icy_vidshow(data, title) +% h_fig = icy_vidshow(h_fig, data) +% h_fig = icy_vidshow(h_fig, data, title) +% +% Display the 2D+T image 'data' in Icy, and return the handle of the +% corresponding figure. +% +% If the 'h_fig' argument is provided, the corresponding figure is used; +% otherwise, a new figure is created. If the 'title' argument is provided, +% the function will also change the title of the figure, otherwise it is let +% unchanged. + +% Allocate a new figure if necessary +if(~exist('title', 'var') && exist('data', 'var') && ischar(data)) + title = data; + data = h_fig; + h_fig = icy_figure(); +elseif(~exist('data', 'var')) + data = h_fig; + h_fig = icy_figure(); +end + +% Default title +persistent counter; +if(isempty(counter)) + counter = 0; +end +if(~exist('title', 'var')) + title = icy_gettitle(h_fig); + if(isempty(title)) + counter = counter + 1; + title = sprintf('Video %d', counter); + end +end + +% Execute the command +args_in.h_fig = int32(h_fig); +args_in.title = title; +args_in.data = data; +icy_command('plugins.ylemontag.matlabxserver.MatlabXServerDeamon', 'vidshow', args_in); diff --git a/src/main/resources/tooltip-Matlab-function-caller.png b/src/main/resources/tooltip-Matlab-function-caller.png new file mode 100644 index 0000000000000000000000000000000000000000..bfcfb9de757eeb8e787ae894aeb0b567fda8ac93 Binary files /dev/null and b/src/main/resources/tooltip-Matlab-function-caller.png differ