commit 1ac99bdcfaab7eb6f4a898ef902792327bccc39a Author: Aljaž Gerečnik Date: Sat Feb 15 10:21:23 2025 +0100 Fixed measurement group tracking UID to make it work with OHIF diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..e69de29 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..d2b0d0e --- /dev/null +++ b/.gitignore @@ -0,0 +1,9 @@ +*~ +OrthancStorage/ +__pycache__/ +config.json +venv/ + +# Those files are automatically downloaded +models/resnet50-11ad3fa6.pth +models/retina_res50_trained_08_03.pth diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..f871c69 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,14 @@ +cff-version: "1.1.0" +message: "If you use this software, please cite it using these metadata." +title: Orthanc +abstract: "Orthanc is a lightweight open-source DICOM server for medical imaging supporting representational state transfer (REST)." +authors: + - + affiliation: UCLouvain + family-names: Jodogne + given-names: "Sébastien" +doi: "10.1007/s10278-018-0082-y" +license: "GPL-3.0-or-later" +repository-code: "https://orthanc.uclouvain.be/hg/orthanc/" +version: 1.12.3 +date-released: 2024-01-31 diff --git a/COPYING b/COPYING new file mode 100644 index 0000000..dba13ed --- /dev/null +++ b/COPYING @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +our General Public Licenses are 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. + + 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. + + Developers that use our General Public Licenses protect your rights +with two steps: (1) assert copyright on the software, and (2) offer +you this License which gives you legal permission to copy, distribute +and/or modify the software. + + A secondary benefit of defending all users' freedom is that +improvements made in alternate versions of the program, if they +receive widespread use, become available for other developers to +incorporate. Many developers of free software are heartened and +encouraged by the resulting cooperation. However, in the case of +software used on network servers, this result may fail to come about. +The GNU General Public License permits making a modified version and +letting the public access it on a server without ever releasing its +source code to the public. + + The GNU Affero General Public License is designed specifically to +ensure that, in such cases, the modified source code becomes available +to the community. It requires the operator of a network server to +provide the source code of the modified version running there to the +users of that server. Therefore, public use of a modified version, on +a publicly accessible server, gives the public access to the source +code of the modified version. + + An older license, called the Affero General Public License and +published by Affero, was designed to accomplish similar goals. This is +a different license, not a version of the Affero GPL, but Affero has +released a new version of the Affero GPL which permits relicensing under +this license. + + 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 Affero 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. Remote Network Interaction; Use with the GNU General Public License. + + Notwithstanding any other provision of this License, if you modify the +Program, your modified version must prominently offer all users +interacting with it remotely through a computer network (if your version +supports such interaction) an opportunity to receive the Corresponding +Source of your version by providing access to the Corresponding Source +from a network server at no charge, through some standard or customary +means of facilitating copying of software. This Corresponding Source +shall include the Corresponding Source for any work covered by version 3 +of the GNU General Public License that is incorporated pursuant to the +following paragraph. + + 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 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 work with which it is combined will remain governed by version +3 of the GNU General Public License. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU Affero 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 Affero 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 Affero 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 Affero 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. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero 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 Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + 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 AGPL, see +. diff --git a/OrthancExplorer.js b/OrthancExplorer.js new file mode 100644 index 0000000..456cd22 --- /dev/null +++ b/OrthancExplorer.js @@ -0,0 +1,129 @@ +/** + * Orthanc plugin for mammography + * Copyright (C) 2024 Edouard Chatzopoulos and Sebastien Jodogne, + * ICTEAM UCLouvain, Belgium + * + * This program is free software: you can redistribute it and/or + * modify it under the terms of the GNU Affero 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 + * Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero General Public License + * along with this program. If not, see . + **/ + +var mammographyButton = null; + +$('#instance').live('pagecreate', function() { + mammographyButton = $('') + .attr('data-role', 'button') + .attr('href', '#') + .attr('data-icon', 'search') + .attr('data-theme', 'e') + .text('Deep learning for mammography'); + + mammographyButton.insertBefore($('#instance-delete').parent().parent()); + + mammographyButton.click(function() { + if ($.mobile.pageData) { + $.ajax({ + type: 'POST', + url: '../mammography-apply', + dataType: 'json', + contentType: 'application/json', + data: JSON.stringify({ + 'instance' : $.mobile.pageData.uuid, + }), + cache: false, + success: function(result) { + console.log(result); + window.location.assign('explorer.html#series?uuid=' + result.ParentSeries); + }, + error: function() { + alert('Cannot apply deep learning model'); + } + }); + } + }); +}); + +$('#instance').live('pagebeforeshow', function() { + mammographyButton.hide(); +}); + +$('#instance').live('pageshow', function() { + $.ajax({ + url: '../instances/' + $.mobile.pageData.uuid + '/tags?simplify', + dataType: 'json', + cache: false, + success: function(tags) { + if (tags.Modality == 'MG') { + mammographyButton.show(); + } + } + }); +}); + + +$('#study').live('pagebeforecreate', function() { + var b = $('') + .attr('data-role', 'button') + .attr('href', '#') + .attr('data-icon', 'search') + .attr('data-theme', 'e') + .text('Stone Web Viewer (for mammography)'); + + b.insertBefore($('#study-delete').parent().parent()); + b.click(function() { + if ($.mobile.pageData) { + $.ajax({ + url: '../studies/' + $.mobile.pageData.uuid, + dataType: 'json', + cache: false, + success: function(study) { + var studyInstanceUid = study.MainDicomTags.StudyInstanceUID; + window.open('../mammography-viewer/index.html?study=' + studyInstanceUid); + } + }); + } + }); +}); + + +$('#series').live('pagebeforecreate', function() { + var b = $('') + .attr('data-role', 'button') + .attr('href', '#') + .attr('data-icon', 'search') + .attr('data-theme', 'e') + .text('Stone Web Viewer (for mammography)'); + + b.insertBefore($('#series-delete').parent().parent()); + b.click(function() { + if ($.mobile.pageData) { + $.ajax({ + url: '../series/' + $.mobile.pageData.uuid, + dataType: 'json', + cache: false, + success: function(series) { + $.ajax({ + url: '../studies/' + series.ParentStudy, + dataType: 'json', + cache: false, + success: function(study) { + var studyInstanceUid = study.MainDicomTags.StudyInstanceUID; + var seriesInstanceUid = series.MainDicomTags.SeriesInstanceUID; + window.open('../mammography-viewer/index.html?study=' + studyInstanceUid + + '&series=' + seriesInstanceUid); + } + }); + } + }); + } + }); +}); \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..d5432e4 --- /dev/null +++ b/README.md @@ -0,0 +1,124 @@ +Mammography plugin for Orthanc +============================== + +This plugin for [Orthanc](https://orthanc.uclouvain.be/) adds a **deep +learning algorithm to detect masses in scanned mammograms**. The inference +algorithm produces DICOM-SR (structured reports) instances that are +stored inside Orthanc. The DICOM-SR instance can then be displayed +using a version of the [Stone Web viewer for +Orthanc](https://www.orthanc-server.com/static.php?page=stone-web-viewer). + +[Reference paper](https://ebooks.iospress.nl/doi/10.3233/SHTI240603), +in the BibTeX format: + +```BibTeX +@inproceedings{OrthancMIE2024, + title = {Integrated and Interoperable Platform for Detecting Masses on Mammograms}, + author = {Chatzopoulos, Edouard and Jodogne, S\'ebastien}, + booktitle = {34th Medical Informatics Europe Conference (MIE 2024)}, + address = {Athens, Greece}, + journal = {Studies in Health Technology and Informatics}, + volume = {316}, + pages = {1103-1107}, + issn = {1879-8365}, + doi = {10.3233/SHTI240603}, + publisher = {{IOS} Press}, + year = {2024} +} +``` + +This plugin is copyrighted by the UCLouvain university, under the +AGPLv3+ license. It is a deliverable of the research lab led by +[Sébastien Jodogne](https://info.ucl.ac.be/~sjodogne/). + +![Example](viewer/2024-03-09-FirstDicomSR.png) + + +Setup +----- + +Make sure that Python 3 is installed with support of [virtual +environments](https://docs.python.org/3/library/venv.html). Under +Debian/Ubuntu distributions, this can be done by running: + +``` +$ sudo apt update +$ sudo apt install python3 python3-venv +``` + +Evidently, you also have to [install +Orthanc](https://www.orthanc-server.com/download.php). The mammography +plugin requires the two following plugins for Orthanc to be installed: + +* [Python plugin](https://orthanc.uclouvain.be/book/plugins/python.html). +* [DICOMweb plugin](https://orthanc.uclouvain.be/book/plugins/dicomweb.html), if you want to use the DICOM-SR viewer. + + +Configuration +------------- + +Firstly, clone this repository: + +``` +$ cd /tmp/ +$ git clone https://github.com/jodogne/orthanc-mammography/ +``` + +Secondly, setup the Python virtual environment with the required +dependencies: + +``` +$ cd /tmp/orthanc-mammography/ +$ python3 -m venv venv +$ source ./venv/bin/activate +(venv) python3 -m pip install --upgrade pip +(venv) python3 -m pip install -r requirements.txt +``` + +Thirdly, create a [configuration +file](https://orthanc.uclouvain.be/book/plugins/dicomweb.html#installation) +for Orthanc with Python. A minimalist configuration file would look +like (make sure to adapt the path to the virtual environment, +depending on your version of Python): + +```json +{ + "Plugins" : [ + "...list of paths to the Python and DICOMweb plugins..." + ], + "Python" : { + "Path" : "./mammography.py" + }, + "Mammography" : { + "VirtualEnv" : "./venv/lib/python3.10/site-packages/" + } +} +``` + +Finally, start Orthanc using this configuration file. + + +Usage +----- + +Two samples images from the [CBIS-DDSM +dataset](https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=22516629) +are available in the [`./sample-images/` folder](./sample-images/). + +[Upload DICOM images of mammograms to +Orthanc](https://orthanc.uclouvain.be/book/users/cookbook.html#uploading-dicom-files). + +Using the built-in [Orthanc +Explorer](http://localhost:8042/app/explorer.html) interface of +Orthanc, go down in the DICOM hierarchy until you reach a DICOM +instance whose modality is `MG` (mammogram). The yellow button `Deep +learning for mammography` will appear. + +Clicking on the button will launch the deep learning inference. Once +the inference is done (this takes about 5 seconds on a standard +laptop), Orthanc Explorer is automatically redirected to the +newly-created DICOM series that contains the DICOM-SR instance with +the results of the inference. + +You can then click on the yellow button `Stone Web viewer (for +mammography)` to display the content of the DICOM-SR. diff --git a/dicom_sr.py b/dicom_sr.py new file mode 100644 index 0000000..78a7b63 --- /dev/null +++ b/dicom_sr.py @@ -0,0 +1,101 @@ +# Orthanc plugin for mammography +# Copyright (C) 2024 Edouard Chatzopoulos and Sebastien Jodogne, +# ICTEAM UCLouvain, Belgium +# +# This program is free software: you can redistribute it and/or +# modify it under the terms of the GNU Affero 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 +# Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see . + + +import highdicom +import model +import numpy +import pydicom +import time +from datetime import datetime + + +def CreateProbabilityOfCancer(probability): + assert(probability >= 0 and probability <= 100) + + return [ + highdicom.sr.Measurement( + name = pydicom.sr.codedict.codes.DCM.ProbabilityOfCancer, + value = probability, + unit = pydicom.sr.codedict.codes.UCUM.Percent, + ), + ] + + +def apply(retina_net, dicom, + minimum_score = 0.2, + title = 'Orthanc Deep Learning for Mammography'): + start = time.time() + result = model.apply_model_to_dicom(retina_net, dicom, rescale_boxes=True) + end = time.time() + print('Time: %.02f seconds' % (end - start)) + + assert(len(result['boxes']) == len(result['scores'])) + + # Generic X-ray report, added in DICOM 2023c, so not directly + # available in pydicom and in DicomSRValidator: + # https://dicom.nema.org/medical/dicom/2023c/output/chtml/part16/sect_CID_100.html + reportedProcedure = pydicom.sr.coding.Code(value = '43468-8', + scheme_designator = 'LN', + meaning = 'XR unspecified body region') + + observation_context = highdicom.sr.ObservationContext() + + planar_groups = [] + + for i in range(len(result['boxes'])): + score = result['scores'][i].detach().numpy() + if score > minimum_score: + box = result['boxes'][i].detach().numpy() + assert(len(box) == 4) + + (x1, y1, x2, y2) = box + + planar_groups.append(highdicom.sr.PlanarROIMeasurementsAndQualitativeEvaluations( + referenced_region = highdicom.sr.ImageRegion( + graphic_type = highdicom.sr.GraphicTypeValues.POLYLINE, + graphic_data = numpy.array([ [x1, y1], [x2, y1], [x2, y2], [x1,y2], [x1,y1] ]), + source_image = highdicom.sr.SourceImageForRegion.from_source_image(dicom, referenced_frame_numbers = None), + ), + tracking_identifier = highdicom.sr.TrackingIdentifier( + identifier = title, + uid = highdicom.UID(), + ), + # 'SCT' means 'SNOMED-CT' + # geometric_purpose = highdicom.sr.CodedConcept('75958009', 'SCT', 'Bounded by'), + measurements = CreateProbabilityOfCancer(score * 100.0), + )) + + measurement_report = highdicom.sr.MeasurementReport( + observation_context = observation_context, + procedure_reported = reportedProcedure, + imaging_measurements = planar_groups, + ) + + sr_object = highdicom.sr.ComprehensiveSR( + evidence = [ dicom ], + content = measurement_report, + series_number = 1, + series_instance_uid = highdicom.UID(), + sop_instance_uid = highdicom.UID(), + instance_number = 1 + ) + + sr_object.SeriesDate = datetime.now().strftime("%Y%m%d") + sr_object.SeriesTime = datetime.now().strftime("%H%M%S") + + return sr_object diff --git a/download.py b/download.py new file mode 100644 index 0000000..e30fa22 --- /dev/null +++ b/download.py @@ -0,0 +1,76 @@ +# Orthanc plugin for mammography +# Copyright (C) 2024 Edouard Chatzopoulos and Sebastien Jodogne, +# ICTEAM UCLouvain, Belgium +# +# This program is free software: you can redistribute it and/or +# modify it under the terms of the GNU Affero 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 +# Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see . + + +import hashlib +import io +import os +import requests +import sys + +def get(target, url, expected_size, expected_md5): + print('Downloading: %s' % url) + + if os.path.isfile(target): + with open(target, 'rb') as f: + content = f.read() + + if (len(content) == expected_size and + hashlib.md5(content).hexdigest() == expected_md5): + print(' File already downloaded') + return + else: + raise Exception('Target file already exists with bad content, please remove it: %s' % target) + + r = requests.get(url, stream = True) + r.raise_for_status() + + content_length = int(r.headers['Content-Length']) + if content_length != expected_size: + raise Exception('Bad file size on the server: %d (actual) vs. %d (expected)' % (content_length, expected_size)) + + bar_width = 30 + + with io.BytesIO() as f: + progress = 0 + + for chunk in r.iter_content(chunk_size = 1024 * 1024): + f.write(chunk) + + progress += len(chunk) + percent = float(progress) / float(content_length) + sys.stdout.write('\r') + sys.stdout.write(' Completed: [{:{}}] {:>3}%' + .format('=' * round(percent * float(bar_width)), + bar_width, round(percent * 100.0))) + sys.stdout.flush() + + sys.stdout.write('\n') + sys.stdout.flush() + + f.seek(0) + content = f.read() + + if len(content) != expected_size: + raise Exception('Server has not returned the expected number of bytes: %d (actual) vs. %d (expected)' % (len(content), expected_size)) + + actual_md5 = hashlib.md5(content).hexdigest() + if actual_md5 != expected_md5: + raise Exception('Bad MD5 checksum: %s (actual) vs. %s (expected)' % (actual_md5, expected_md5)) + + with open(target, 'wb') as f: + f.write(content) diff --git a/mammography.py b/mammography.py new file mode 100644 index 0000000..61cc9e7 --- /dev/null +++ b/mammography.py @@ -0,0 +1,137 @@ +# Orthanc plugin for mammography +# Copyright (C) 2024 Edouard Chatzopoulos and Sebastien Jodogne, +# ICTEAM UCLouvain, Belgium +# +# This program is free software: you can redistribute it and/or +# modify it under the terms of the GNU Affero 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 +# Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see . + + +## +## Initialize the virtual environment for pytorch. +## DO NOT add other "import" in this section! +## + +import sys +import json +import orthanc + +config = json.loads(orthanc.GetConfiguration()).get('Mammography', {}) +venv = config.get('VirtualEnv') + +if venv != None: + # https://orthanc.uclouvain.be/book/plugins/python.html#working-with-virtual-environments + sys.path.insert(0, venv) + + +## +## Install the Stone Web viewer +## + +STONE_VERSION = '2024-08-31-StoneWebViewer-DICOM-SR' +VIEWER_PREFIX = '/mammography-viewer/' + +import os +SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__)) +VIEWER_DIR = os.path.join(SCRIPT_DIR, 'viewer') + +sys.path.append(os.path.join(SCRIPT_DIR, '..')) +import download + +os.makedirs(VIEWER_DIR, exist_ok = True) + +download.get(os.path.join(VIEWER_DIR, '%s.zip' % STONE_VERSION), + 'https://github.com/jodogne/orthanc-mammography/raw/master/viewer/%s.zip' % STONE_VERSION, + 4815178, '86b52a17f86e4769d12e9ae680c4a99f') + +import zipfile +stone_assets = zipfile.ZipFile(os.path.join(VIEWER_DIR, '%s.zip' % STONE_VERSION)) + +MIME_TYPES = { + '.css' : 'text/css', + '.gif' : 'image/gif', + '.html' : 'text/html', + '.jpeg' : 'image/jpeg', + '.js' : 'text/javascript', + '.png' : 'image/png', +} + +def serve_stone_web_viewer(output, uri, **request): + if not uri.startswith(VIEWER_PREFIX): + output.SendHttpStatusCode(404) + elif request['method'] != 'GET': + output.SendMethodNotAllowed('GET') + else: + try: + path = '%s/%s' % (STONE_VERSION, uri[len(VIEWER_PREFIX):]) + extension = os.path.splitext(path) [1] + if not extension in MIME_TYPES: + mime = 'application/octet-stream' + else: + mime = MIME_TYPES[extension] + + with stone_assets.open(path) as f: + output.AnswerBuffer(f.read(), mime) + except: + output.SendHttpStatusCode(500) + + +orthanc.RegisterRestCallback('%s(.*)' % VIEWER_PREFIX, serve_stone_web_viewer) + + +## +## Load the deep learning model +## + +import highdicom +import io +import os +import pydicom + +sys.path.append(os.path.join(SCRIPT_DIR, '..')) +import model +import dicom_sr + +orthanc.LogWarning('Loading the RetinaNet model for mammography') +my_retina_net = model.load_retina_net() + + +## +## Install the Orthanc Explorer extension +## + +with open(os.path.join(SCRIPT_DIR, 'OrthancExplorer.js'), 'r') as f: + orthanc.ExtendOrthancExplorer(f.read()) + +def execute_inference(output, uri, **request): + if request['method'] != 'POST': + output.SendMethodNotAllowed('POST') + else: + body = json.loads(request['body']) + + f = orthanc.GetDicomForInstance(body['instance']) + dicom = pydicom.dcmread(io.BytesIO(f)) + + if len(dicom.pixel_array.shape) != 2: + orthanc.LogError('Not a graylevel instance: %s' % body['instance']) + output.SendHttpStatusCode(400) + else: + result = dicom_sr.apply(my_retina_net, dicom, minimum_score=0.2) + + with io.BytesIO() as f: + pydicom.dcmwrite(f, result) + f.seek(0) + content = f.read() + + output.AnswerBuffer(orthanc.RestApiPost('/instances', content), 'application/json') + +orthanc.RegisterRestCallback('/mammography-apply', execute_inference) diff --git a/model.py b/model.py new file mode 100644 index 0000000..ee8ed81 --- /dev/null +++ b/model.py @@ -0,0 +1,181 @@ +# Orthanc plugin for mammography +# Copyright (C) 2024 Edouard Chatzopoulos and Sebastien Jodogne, +# ICTEAM UCLouvain, Belgium +# +# This program is free software: you can redistribute it and/or +# modify it under the terms of the GNU Affero 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 +# Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see . + + +import download + +import os +import numpy as np +import torch +import torch.nn as nn +import torchvision.transforms.v2 as transforms + +from functools import partial +from torchvision.models.detection import RetinaNet +from torchvision.models.detection.anchor_utils import AnchorGenerator +from torchvision.models.detection.backbone_utils import _resnet_fpn_extractor +from torchvision.models.detection.retinanet import RetinaNetHead +from torchvision.models.resnet import resnet50, ResNet50_Weights +from torchvision.ops import FrozenBatchNorm2d +from torchvision.ops.feature_pyramid_network import LastLevelP6P7 + + +SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__)) +MODELS_DIR = os.path.join(SCRIPT_DIR, 'models') + +os.makedirs(MODELS_DIR, exist_ok = True) + +download.get(os.path.join(MODELS_DIR, 'resnet50-11ad3fa6.pth'), + 'https://orthanc.uclouvain.be/downloads/cross-platform/orthanc-mammography/models/2024-03-08-resnet50-11ad3fa6.pth', + 102540417, '012571d812f34f8442473d8b827077b5') + +download.get(os.path.join(MODELS_DIR, 'retina_res50_trained_08_03.pth'), + 'https://orthanc.uclouvain.be/downloads/cross-platform/orthanc-mammography/models/2024-03-08-retina_res50_trained_08_03.pth', + 145735292, '53aa159ea0b83234d767aacb43619748') + + +class ResizeBetter: + def __init__(self, min_size=1750): + self.min_size = min_size + + def __call__(self, sample): + shape = sample[0].shape[-2:] + return transforms.Resize((self.min_size,int(self.min_size*shape[1]/shape[0])), + interpolation=transforms.InterpolationMode.BILINEAR, + antialias=True)(sample) + + +def anchorgen(): + anchor_sizes = tuple((x, int(x * 2 ** (1.0 / 3)), int(x * 2 ** (2.0 / 3))) for x in [32, 64, 128, 256, 512]) + aspect_ratios = ((0.5, 1.0, 2.0),) * len(anchor_sizes) + anchor_generator = AnchorGenerator(anchor_sizes, aspect_ratios) + return anchor_generator + + +def load_model(config, pretrained_path, mean=0, std=1): + if False: + # Download backbone from Internet + model_backbone = resnet50(norm_layer = FrozenBatchNorm2d, + weights=ResNet50_Weights.DEFAULT) + else: + weights = torch.load(os.path.join(MODELS_DIR, 'resnet50-11ad3fa6.pth'), map_location=torch.device('cpu')) + model_backbone = resnet50(norm_layer = FrozenBatchNorm2d) + model_backbone.load_state_dict(weights) + + model_backbone.fc = model_backbone.fc = nn.Sequential( + nn.Linear(4*512 , config["num_classes"]) + ) + + model_backbone = _resnet_fpn_extractor(model_backbone, + config["trainable_backbone_layers"], + returned_layers=[2, 3, 4], + extra_blocks=LastLevelP6P7(2048, 256)) + + anchor_generator = anchorgen() + + head = RetinaNetHead( + model_backbone.out_channels, + anchor_generator.num_anchors_per_location()[0], + config["num_classes"], + norm_layer=partial(nn.GroupNorm, 32), + ) + head.regression_head._loss_type = "giou" + model = RetinaNet(model_backbone, + num_classes=config["num_classes"], + anchor_generator=anchor_generator, + head=head, + min_size=config["min_size"] , + max_size=config["max_size"], + image_mean=[mean, mean, mean], + image_std=[std, std, std], + fg_iou_thresh=config["fg_iou_thresh"], + bg_iou_thresh=config["bg_iou_thresh"], + nms_thresh=config["nms_thresh"], + _skip_resize=True) + + if pretrained_path is not None: + state_dict = torch.load(pretrained_path, map_location=torch.device('cpu')) + model.load_state_dict(state_dict) + print(f"Model loaded from checkpoint {pretrained_path}") + + for layer in model.modules(): + if isinstance(layer, nn.BatchNorm2d) or isinstance(layer, nn.BatchNorm1d): + layer.eval() # Set to evaluation mode + layer.weight.requires_grad = False + layer.bias.requires_grad = False + + model.eval() + return model + + +def load_retina_net(): + config = { + 'num_classes' : 2, + 'min_size' : 2048, + 'max_size' : 2048, + 'trainable_backbone_layers' : 0, + 'fg_iou_thresh' : 0.5, + 'bg_iou_thresh' : 0.4, + 'nms_thresh' : 0.3, + } + + return { + 'min_size' : config['min_size'], + 'eval' : load_model(config, os.path.join(MODELS_DIR, 'retina_res50_trained_08_03.pth')), + } + + +def dicom_to_tensor(dicom, min_size): + assert(len(dicom.pixel_array.shape) == 2) + + #Normalize the value scale to 0-255 (Useful for some processing steps) + im_array = np.stack((dicom.pixel_array,)*3, axis=-1) + im_max = np.max(im_array) + im_min = np.min(im_array) + image_tensor = torch.tensor(im_array.astype(np.float32).transpose(2, 0, 1)) + + #Resize longest side to 2048 (with same ratio) and normalize + image_tensor = ResizeBetter(min_size) (image_tensor) + + std = torch.std(image_tensor) + mean = torch.mean(image_tensor) + image_tensor = torch.sub(image_tensor, mean ) + image_tensor = torch.div(image_tensor, std) + + assert(len(image_tensor.shape) == 3) + + return image_tensor + + +def apply_model_to_dicom(model, dicom, rescale_boxes=True): + image_tensor = dicom_to_tensor(dicom, model['min_size']) + output = model['eval'] ([ image_tensor ]) + + assert(len(output) == 1) + output = output[0] + + if rescale_boxes: + originalWidth = dicom.pixel_array.shape[1] + originalHeight = dicom.pixel_array.shape[0] + resizedWidth = image_tensor.shape[2] + resizedHeight = image_tensor.shape[1] + + # TODO - The "int()" in ResizeBetter is anisotropic + ratio = originalWidth / resizedWidth + output['boxes'] *= ratio + + return output diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..377b4b1 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,7 @@ +highdicom==0.22.0 +numpy==2.1.0 +opencv-python==4.10.0.84 +pydicom==2.4.4 +torch==2.3.0 +torchaudio==2.3.0 +torchvision==0.18.0 diff --git a/sample-images/P_00009_RIGHT_CC.dcm b/sample-images/P_00009_RIGHT_CC.dcm new file mode 100644 index 0000000..64c20a9 Binary files /dev/null and b/sample-images/P_00009_RIGHT_CC.dcm differ diff --git a/sample-images/P_00009_RIGHT_MLO.dcm b/sample-images/P_00009_RIGHT_MLO.dcm new file mode 100644 index 0000000..2989feb Binary files /dev/null and b/sample-images/P_00009_RIGHT_MLO.dcm differ diff --git a/sample-images/P_00021_LEFT_CC.dcm b/sample-images/P_00021_LEFT_CC.dcm new file mode 100644 index 0000000..70d4830 Binary files /dev/null and b/sample-images/P_00021_LEFT_CC.dcm differ diff --git a/sample-images/P_00021_LEFT_MLO.dcm b/sample-images/P_00021_LEFT_MLO.dcm new file mode 100644 index 0000000..1c52876 Binary files /dev/null and b/sample-images/P_00021_LEFT_MLO.dcm differ diff --git a/viewer/2024-03-09-FirstDicomSR.png b/viewer/2024-03-09-FirstDicomSR.png new file mode 100644 index 0000000..c6304a2 Binary files /dev/null and b/viewer/2024-03-09-FirstDicomSR.png differ diff --git a/viewer/2024-03-15-StoneWebViewer-DICOM-SR.zip b/viewer/2024-03-15-StoneWebViewer-DICOM-SR.zip new file mode 100644 index 0000000..932bb18 Binary files /dev/null and b/viewer/2024-03-15-StoneWebViewer-DICOM-SR.zip differ diff --git a/viewer/2024-08-31-StoneWebViewer-DICOM-SR.zip b/viewer/2024-08-31-StoneWebViewer-DICOM-SR.zip new file mode 100644 index 0000000..1f95c53 Binary files /dev/null and b/viewer/2024-08-31-StoneWebViewer-DICOM-SR.zip differ