From e2e2d9e220158aa2fd7dd0f4995c76d7d09ae79b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tor-bj=C3=B6rn=20Claesson?= <tclaesson@gmail.com>
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 <me@tobias.gr>
---
 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