| Message ID | 877cxyp1wf.fsf@gmail.com |
|---|---|
| State | New |
| Headers | show |
| Series | [bug#60640] Gnu: Add gdcm | expand |
Hi! This patch adds GDCM (a nice C++ library for DICOM, as in medical imaging), with a few wharts: 1. I have not yet been able to build the bin output, which consists of utilities for manipulating DICOM data. 2. It does not build pdf-documentation, since that would require texlive as a native input. 3. It does not perform tests. 4. It uses socketxx, ljpeg and papyrus3 from the gdcm sources. 5. I'm not sure how to specify util-linux:bin as an input? Cheers, Tor-björn Claesson help-debbugs@gnu.org (GNU bug Tracking System) writes: > Thank you for filing a new bug report with debbugs.gnu.org. > > This is an automatically generated reply to let you know your message > has been received. > > Your message is being forwarded to the package maintainers and other > interested parties for their attention; they will reply in due course. > > Your message has been sent to the package maintainer(s): > guix-patches@gnu.org > > If you wish to submit further information on this problem, please > send it to 60640@debbugs.gnu.org. > > Please do not send mail to help-debbugs@gnu.org unless you wish > to report a problem with the Bug-tracking system.
Den sön 8 jan. 2023 kl 10:00 skrev Tor-björn Claesson <tclaesson@gmail.com>: > > 5. I'm not sure how to specify util-linux:bin as an input? > I mean util-linux:lib...
Hi Tor-björn, On 8 January 2023 08:04:40 UTC, "Tor-björn Claesson" <tclaesson@gmail.com> wrote: >Den sön 8 jan. 2023 kl 10:00 skrev Tor-björn Claesson <tclaesson@gmail.com>: > >> >> 5. I'm not sure how to specify util-linux:bin as an input? >> >I mean util-linux:lib... Exactly like you did. Are you seeing util-linux-related failures? Kind regards, T G-R Sent on the go. Excuse or enjoy my brevity.
Hi Tobias, thanks for taking the time to comment! Tobias Geerinckx-Rice <me@tobias.gr> writes: > Hi Tor-björn, > > On 8 January 2023 08:04:40 UTC, "Tor-björn Claesson" <tclaesson@gmail.com> wrote: >>Den sön 8 jan. 2023 kl 10:00 skrev Tor-björn Claesson <tclaesson@gmail.com>: >> >>> >>> 5. I'm not sure how to specify util-linux:bin as an input? >>> >>I mean util-linux:lib... > > Exactly like you did. Are you seeing util-linux-related failures? > > > Kind regards, > > T G-R > > Sent on the go. Excuse or enjoy my brevity. No failures, only guix lint tells me "gdcm@3.0.20: label 'util-linux' does not match package name 'util-linux:lib'", so I thought I might be doing something wrong. If not then all fine on that front.
On Mon Jan 9, 2023 at 10:50 AM GMT, Tor-björn Claesson wrote: > No failures, only guix lint tells me "gdcm@3.0.20: label 'util-linux' > does not match package name 'util-linux:lib'", so I thought I might be > doing something wrong. If not then all fine on that front. Oh, that's fine. I don't think there's a way to fix that at the moment. -- (
Hi again, Tor-björn Claesson 写道： > This patch adds GDCM (a nice C++ library for DICOM, as in > medical imaging), > with a few wharts: I'll answer your questions later, but have started the build before I go out. The build appears to be running something like until fc-something; do :; done in an infinite loop, spamming the build log at best and slowing down the build at worst. Did you notice that too? Kind regards, T G-R
Hi! I'll answer your questions later, but have started the build > before I go out. > > The build appears to be running something like > > until fc-something; do :; done > > in an infinite loop, spamming the build log at best and slowing > down the build at worst. > > Did you notice that too? > I get a lot of "Fontconfig error: No writable cache directories" which appeared after adding graphviz as a native input for building documentation. Is this what you are meaning? Thanks=) Tor-björn
Hi! Tor-björn Claesson <tclaesson@gmail.com> skribis: > This patch adds GDCM (a nice C++ library for DICOM, as in medical imaging), > with a few wharts: Commit 15caeb745c5d77b69905d38d43b4d09742bc71b6, pushed a couple of days ago, adds GDCM (although the patch was much older). Could you check if anything’s missing compared to your version? Thanks, Ludo’.
Hi! Ludovic Courtès <ludo@gnu.org> writes: > > Commit 15caeb745c5d77b69905d38d43b4d09742bc71b6, pushed a couple of days > ago, adds GDCM (although the patch was much older). > > Could you check if anything’s missing compared to your version? > > Thanks, > Ludo’. Yes, that was great! The pushed patch is version 2.8, whereas my patch is version 3.0. I was able to port my application to 2.8 in 3 minutes, so I don't notice big functional differences=) Also it does tests, which I did not get to work yet, but it does not specify system libraries. Cheers, Tor-björn Claesson
Hi, Tor-björn Claesson <tclaesson@gmail.com> skribis: > The pushed patch is version 2.8, whereas my patch is version 3.0. I was > able to port my application to 2.8 in 3 minutes, so I don't notice big > functional differences=) > > Also it does tests, which I did not get to work yet, but it does not > specify system libraries. Could you send (in this issue) one patch that updates to 3.0, and another one to use system libraries? That’d be perfect! Thanks in advance, Ludo’.
Hi, Den lör 14 jan. 2023 kl 01:50 skrev Ludovic Courtès <ludo@gnu.org>: > > Could you send (in this issue) one patch that updates to 3.0, and > another one to use system libraries? > I have a working update to 3.0.20. Except for other possible differences, GDCM changes the name of the include directory between versions; I have to e.g. #include <gdcm-2.8/gdcmImage.h> vs. <gdcm-3.0/gdcmImage.h>. How should we deal with this? Would it make sense to leave a gdcm-2.8 package, to cater for users of the older version, or should we expect people to follow along? Best regards! Tor-björn
Hi, GDCM was added back in 2022 by the commit 15caeb745c5d77b69905d38d43b4d09742bc71b6. --8<---------------cut here---------------start------------->8--- 15caeb745c5d77b69905d38d43b4d09742bc71b6 Author: Antero Mejr <antero@mailbox.org> AuthorDate: Wed Jun 15 15:39:53 2022 +0000 Commit: Ludovic Courtès <ludo@gnu.org> CommitDate: Sun Jan 8 16:11:45 2023 +0100 gnu: Add gdcm. * gnu/packages/bioinformatics.scm (gdcm): New variable. --8<---------------cut here---------------end--------------->8--- And it's on the 3.0.20. Closing as already availale. Thanks, Oleg
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index 70c820e76b..271593b5f9 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -99,6 +99,7 @@ (define-module (gnu packages image-processing) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages video) + #:use-module (gnu packages web) #:use-module (gnu packages xiph) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) @@ -1776,3 +1777,74 @@ (define-public charls to have them encoded to JPEG-LS, or JPEG-LS streams, which CharLS will decode to images.") (license license:bsd-3))) + +(define-public gdcm + (package + (name "gdcm") + (version "3.0.20") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/malaterre/GDCM/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i")))) + (build-system cmake-build-system) + (outputs '("out" "doc")) + (arguments + (list #:tests? #f + #:phases #~(modify-phases %standard-phases + (add-before 'configure 'set-LDFLAGS + (lambda* (#:key inputs outputs #:allow-other-keys) + (setenv "LDFLAGS" + (string-append "-Wl,-rpath=" + #$output "/lib")))) + (add-before 'build 'patch-gdcm-charls.h + (lambda _ + (substitute* "../source/Utilities/gdcm_charls.h" + (("# include <CharLS/charls.h>") + "# include <charls/charls.h>")) #t))) + #:configure-flags #~(list "-DCMAKE_SKIP_RPATH:BOOL=YES" + "-DCMAKE_BUILD_TYPE:STRING=Release" + "-DCMAKE_C_FLAGS=-fvisibility=hidden" + "-DCMAKE_CXX_FLAGS=-fvisibility=hidden" + "-DGDCM_BUILD_SHARED_LIBS:BOOL=ON" + "-DGDCM_DOCUMENTATION:BOOL=ON" + "-DGDCM_USE_SYSTEM_EXPAT:BOOL=ON" + "-DGDCM_USE_SYSTEM_ZLIB:BOOL=ON" + "-DGDCM_USE_SYSTEM_CHARLS:BOOL=ON" + "-DGDCM_USE_SYSTEM_POPPLER:BOOL=ON" + "-DGDCM_USE_SYSTEM_LIBXML2:BOOL=ON" + "-DGDCM_USE_SYSTEM_JSON:BOOL=ON" + "-DGDCM_USE_SYSTEM_UUID:BOOL=ON" + "-DGDCM_USE_SYSTEM_OPENJPEG:BOOL=ON" + "-DGDCM_USE_SYSTEM_OPENSSL:BOOL=ON" + "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF" + "-DGCM_BUILD_TESTING:BOOL=OFF" + "-DGDCM_BUILD_APPLICATIONS:BOOL=OFF" + "-DGDCM_USE_SYSTEM_PAPYRUS3:BOOL=OFF" + "-DGDCM_USE_SYSTEM_SOCKETXX:BOOL=OFF" + "-DGDCM_USE_SYSTEM_LJPEG:BOOL=OFF"))) + (inputs (list openssl + expat + charls + poppler + libxml2 + json-c + openjpeg + `(,util-linux "lib") + zlib)) + (native-inputs (list git pkg-config doxygen graphviz)) + (home-page "https://gdcm.sourceforge.net") + (synopsis + "C++ library dedicated to reading/parsing and writing DICOM medical files") + (description + "Grassroots DICOM (GDCM) is an implementation of the DICOM standard +designed to be open source so that researchers may access clinical data +directly. GDCM includes a file format definition and a network communications +protocol, both of which should be extended to provide a full set of tools for +a researcher or small medical imaging vendor to interface with an existing +medical database.") + (license license:bsd-3)))