Expanded tractography file format support

cmake/Dependencies.cmake

@@ -276,3 +276,47 @@ else()
     )
     FetchContent_MakeAvailable(magic_enum)
 endif()
+
+# libzip — required by the TRX tractography format handler for reading and
+# writing (un)compressed zip archives. A system install is mandatory: the build
+# environment may be offline, so FetchContent is not used here; the system
+# package (which itself pulls in zlib for the deflate codec) is located through
+# its CMake config package where available.
+#
+# Some distributions ship a libzip CMake config package whose imported-target
+# existence checks reference the libzip command-line tools (zipcmp/zipmerge/
+# ziptool); when only the runtime library + headers are installed those checks
+# raise a fatal error on include(). We therefore probe the config package only
+# when the user opts in (MRTRIX_USE_SYSTEM_LIBZIP_CONFIG) and otherwise locate
+# the shared library and headers directly (optionally via pkg-config),
+# synthesising the libzip::zip target ourselves.
+option(MRTRIX_USE_SYSTEM_LIBZIP_CONFIG "Use the system libzip CMake config package" OFF)
+if(MRTRIX_USE_SYSTEM_LIBZIP_CONFIG)
+    find_package(libzip CONFIG REQUIRED)
+endif()
+if(NOT TARGET libzip::zip)
+    find_package(PkgConfig QUIET)
+    if(PkgConfig_FOUND)
+        pkg_check_modules(PC_LIBZIP QUIET libzip)
+    endif()
+    find_path(LIBZIP_INCLUDE_DIR
+        NAMES zip.h
+        HINTS ${PC_LIBZIP_INCLUDEDIR} ${PC_LIBZIP_INCLUDE_DIRS}
+        PATHS /usr/include /usr/local/include
+    )
+    find_library(LIBZIP_LIBRARY
+        NAMES zip
+        HINTS ${PC_LIBZIP_LIBDIR} ${PC_LIBZIP_LIBRARY_DIRS}
+        PATHS /usr/lib /usr/local/lib /usr/lib/x86_64-linux-gnu
+    )
+    if(NOT LIBZIP_INCLUDE_DIR OR NOT LIBZIP_LIBRARY)
+        message(FATAL_ERROR
+            "Could not find libzip. Install the libzip development package "
+            "(headers + shared library) or its CMake config package.")
+    endif()
+    add_library(libzip::zip UNKNOWN IMPORTED)
+    set_target_properties(libzip::zip PROPERTIES
+        IMPORTED_LOCATION "${LIBZIP_LIBRARY}"
+        INTERFACE_INCLUDE_DIRECTORIES "${LIBZIP_INCLUDE_DIR}"
+    )
+endif()

cmake/DownloadFiles.cmake

@@ -0,0 +1,39 @@
+# Script-mode helper that downloads a fixed subset of files from a common base URL.
+#
+# Intended to be invoked via "cmake -P" as the DOWNLOAD_COMMAND of an
+# ExternalProject so that the files are fetched at build time (only when tests
+# are built) rather than at configure time. Required variables, passed on the
+# command line with -D:
+#   BASE_URL : URL prefix shared by every file (no trailing slash)
+#   FILES    : "|"-separated list of file names to append to BASE_URL
+#   DEST_DIR : directory into which the files are written (created if absent)
+#
+# Each file is fetched only when not already present, so a partially-completed
+# download step resumes cheaply on the next build without re-fetching whole files.
+
+if(NOT DEFINED BASE_URL OR NOT DEFINED FILES OR NOT DEFINED DEST_DIR)
+    message(FATAL_ERROR "DownloadFiles.cmake requires BASE_URL, FILES and DEST_DIR")
+endif()
+
+file(MAKE_DIRECTORY ${DEST_DIR})
+
+# FILES is delimited with "|" rather than the CMake list separator ";" so that it
+# survives transit as a single command-line argument.
+string(REPLACE "|" ";" file_list "${FILES}")
+
+foreach(file_name IN LISTS file_list)
+    set(target "${DEST_DIR}/${file_name}")
+    if(EXISTS ${target})
+        continue()
+    endif()
+    set(url "${BASE_URL}/${file_name}")
+    message(STATUS "Downloading ${url}")
+    file(DOWNLOAD ${url} ${target} STATUS download_status)
+    list(GET download_status 0 download_code)
+    if(NOT download_code EQUAL 0)
+        list(GET download_status 1 download_message)
+        # Remove the truncated artefact so a re-run does not treat it as complete.
+        file(REMOVE ${target})
+        message(FATAL_ERROR "Failed to download ${url}: ${download_message}")
+    endif()
+endforeach()

cpp/cmd/afdconnectivity.cpp

@@ -20,11 +20,11 @@
 #include "command.h"
 #include "dwi/fmls.h"
 #include "dwi/tractography/SIFT/model_base.h"
-#include "dwi/tractography/file.h"
 #include "dwi/tractography/mapping/loader.h"
 #include "dwi/tractography/mapping/mapper.h"
 #include "dwi/tractography/mapping/mapping.h"
 #include "dwi/tractography/properties.h"
+#include "dwi/tractography/tractogram.h"
 #include "memory.h"
 #include "mrtrix_version.h"
 
@@ -166,7 +166,7 @@ class AFDConnectivity : public DWI::Tractography::SIFT::ModelBase<AFDConnFixel>
 value_type AFDConnectivity::get(const std::filesystem::path &path) {
 
   Tractography::Properties properties;
-  Tractography::Reader<value_type> reader(path, properties);
+  auto reader = Tractography::Tractogram<float>::open(path, properties);
   const size_t track_count = (properties.find("count") == properties.end() ? 0 : to<size_t>(properties["count"]));
   DWI::Tractography::Mapping::TrackLoader loader(reader, track_count, "summing apparent fibre density within track");