Subject: Re: [bug#60640] Gnu: Add gdcm

From: Tobias Geerinckx-Rice <[email-masked]>
Date: Tue, 10 Jan 2023 15:52:49 +0100

Tor-björn Claesson 写道：
> 1. I have not yet been able to build the bin output,
> which consists of utilities for manipulating DICOM data. 

OK, I'll take a look.

> 2. It does not build pdf-documentation, since that would require
> texlive as a native input.

OK.  You can add this sort of information as a comment by the 
relevant line, so it doesn't get lost (even during review :-).

> 3. It does not perform tests.

OK, I'll take a look.

If tests are disabled, the reason should always be noted in a 
comment.  Even if it's just ‘; no test suite’.

> 4. It uses socketxx, ljpeg and papyrus3 from the gdcm sources.

Here too I've punted on that by just adding a comment for now.

> +(define-public gdcm

It used to be common to unconditionally add packages to the end of 
files, but this needlessly increased the risk of merge conflicts.

Instead, just add them wherever they first fit alphabetically; 
here, I put it above ‘mia’.

> +    (version "3.0.20")

‘guix lint’ says this can be updated to 3.1.0 but I didn't try, as 
I'd rather it be tested by an actual user — i.e., you.

> + 
> "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i"))))
> +    (build-system cmake-build-system)
> +    (outputs '("out" "doc"))

/share/doc wasn't actually installed into "doc", but to "out", so 
I set the GDCM_INSTALL_DOC_DIR configure flag.

> +    (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>")

Purely as a matter of taste I dropped the ‘# include ’ from both 
strings and escaped the ‘.’ in the regexp.

> +                               "# include <charls/charls.h>")) 
> #t)))

‘#t’ endings are also obsolete.  Just drop them entirely.  Phases 
can now safely return anything, including nothing or undefined.

I added the following phase to work around log spam, since I 
didn't find its source (nor did I look very hard) [edit: it was 
indeed graphviz, thanks].  By default, $HOME is not writable in 
the build environment.

  (add-before 'build 'set-HOME
    ;; The build spams ‘Fontconfig error: No writable cache
    ;; directories’ in a seemingly endless loop otherwise.
    (lambda _
      (setenv "HOME" "/tmp")))

> +           #:configure-flags #~(list 
> "-DCMAKE_SKIP_RPATH:BOOL=YES"

I, opinionated, added newlines after #:phases and 
#:configure-flags.

Some people like the ‘extreme indentation’ you get by throwing 
away half of your screen width.  I find it leads to cramped code 
and noisy patches once the phases need to get actual work done or 
an even longer CMAKE_ flag comes along.

I also added some newlines and tried to group related flags.

> + 
> "-DCMAKE_C_FLAGS=-fvisibility=hidden"
> + 
> "-DCMAKE_CXX_FLAGS=-fvisibility=hidden"

Should these be explained in a very brief comment?

> + 
> "-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"

Thank you for building with system libraries!  Also remove the 
bundled copies when possible.  I did so in a (rather strict) 
source snippet.

> + 
> "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF"

I cannot get the man pages to build, either.  They need something 
called ‘xsl-ns’.  I've disabled GDCM_BUILD_DOCBOOK_MANPAGES for 
now.

> + 
> "-DGCM_BUILD_TESTING:BOOL=OFF"

Why is this set?  It's reported by CMake as having no effect, and 
a diff of the output confirms that.

> + 
> "-DGDCM_BUILD_APPLICATIONS:BOOL=OFF"

I added a ‘TODO’ comment above these bundled projects:

> + 
> "-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))

Sorted both.

> +    (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.")

I rewrote this just a smidge.  Mostly to remove the extra words, 
and use pretty @acronym{} mark-up.

> +    (license license:bsd-3)))

I still need to check this.

I've attached my WIP V2 to this message, with a commit message 
matching our conventions.

Kind regards,

T G-R

From e2e2d9e220158aa2fd7dd0f4995c76d7d09ae79b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tor-bj=C3=B6rn=20Claesson?= <[email-masked]>
Date: Sat, 7 Jan 2023 21:40:42 +0200
Subject: [PATCH v2] gnu: Add gdcm.

* gnu/packages/image-processing.scm (gdcm): New variable.

Signed-off-by: Tobias Geerinckx-Rice <[email-masked]>
---
 gnu/packages/image-processing.scm | 105 ++++++++++++++++++++++++++++++
 1 file changed, 105 insertions(+)

diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index 70c820e76b..b95cb54964 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)
@@ -196,6 +197,110 @@ (define-public dcmtk
               "A union of the Apache 2.0 licence and various non-copyleft
 licences similar to the Modified BSD licence."))))
 
+(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"))
+              (modules '((guix build utils)
+                         (ice-9 ftw)))
+              (snippet
+               '(begin
+                  (define (unbundle? file)
+                    (and (file-is-directory? file)
+                         ;; Not all directories represent a bundled project,
+                         ;; and some projects can't yet be unbundled.
+                         (not (member file '("." ".."
+                                             "doxygen"
+                                             "gdcmext"
+                                             "gdcmjpeg" ; TODO
+                                             "gdcmrle"
+                                             "socketxx"))))) ; TODO
+                  (with-directory-excursion "Utilities"
+                    (for-each (lambda (utility)
+                                (delete-file-recursively utility)
+                                (substitute* "CMakeLists.txt"
+                                  (((string-append ".*/" utility "/.*")) "")))
+                              (scandir "." unbundle?)))))))
+    (build-system cmake-build-system)
+    (outputs '("out" "doc"))
+    (arguments
+     (list #:tests? #f                  ; XXX
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-before 'configure 'set-LDFLAGS
+                 (lambda* (#:key inputs outputs #:allow-other-keys)
+                   (setenv "LDFLAGS"
+                           (string-append "-Wl,-rpath="
+                                          #$output "/lib"))))
+               (add-before 'build 'set-HOME
+                 ;; The build spams ‘Fontconfig error: No writable cache
+                 ;; directories’ in a seemingly endless loop otherwise.
+                 (lambda _
+                   (setenv "HOME" "/tmp")))
+               (add-before 'build 'patch-gdcm-charls.h
+                 (lambda _
+                   (substitute* "../source/Utilities/gdcm_charls.h"
+                     (("<CharLS/charls\\.h>")
+                      "<charls/charls.h>")))))
+           #:configure-flags
+           #~(list "-DCMAKE_SKIP_RPATH:BOOL=YES"
+                   "-DCMAKE_BUILD_TYPE:STRING=Release"
+                   "-DCMAKE_C_FLAGS=-fvisibility=hidden"
+                   "-DCMAKE_CXX_FLAGS=-fvisibility=hidden"
+                   "-DGDCM_BUILD_SHARED_LIBS:BOOL=ON"
+
+                   "-DGDCM_DOCUMENTATION:BOOL=ON"
+                   "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF" ; TODO? need texlive
+                   (string-append "-DGDCM_INSTALL_DOC_DIR="
+                                  #$output:doc "/share/doc/" #$name)
+                   "-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF" ; TODO: need ‘xsl-ns’
+
+                   "-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_BUILD_APPLICATIONS:BOOL=OFF"
+
+                   ;; TODO: Unbundle these if possible.
+                   "-DGDCM_USE_SYSTEM_PAPYRUS3:BOOL=OFF"
+                   "-DGDCM_USE_SYSTEM_SOCKETXX:BOOL=OFF" ; socketxx in snippet
+                   "-DGDCM_USE_SYSTEM_LJPEG:BOOL=OFF"))) ; gdcmjpeg in snippet
+    (inputs (list charls
+                  expat
+                  json-c
+                  libxml2
+                  openjpeg
+                  openssl
+                  poppler
+                  `(,util-linux "lib")
+                  zlib))
+    (native-inputs (list doxygen git graphviz pkg-config))
+    (home-page "https://gdcm.sourceforge.net")
+    (synopsis "C++ library to read, parse, and write DICOM medical files")
+    (description
+     "@acronym{GDCM, Grassroots DICOM} implements the @acronym{DICOM, Digital
+Imaging and Communications in Medicine} standard to let researchers 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)))
+
 (define-public mia
   (package
     (name "mia")

base-commit: e0ed305f2f096e7048af1a117c72895433f4886a
-- 
2.38.1