Add TRX IO

Dockerfile

@@ -0,0 +1,63 @@
+FROM nvidia/cuda:12.2.2-runtime-ubuntu22.04
+ARG TAG_ANTS
+RUN apt-get update && apt-get full-upgrade -y && \
+  apt-get install --no-install-recommends -y \
+  software-properties-common \
+  unzip \
+  curl \
+  wget \
+  make \
+  git \
+  libboost-all-dev \
+  zlib1g-dev \
+  ca-certificates \
+  qt6-base-dev \
+  qt6-base-dev-tools \
+  qt6-base-private-dev \
+  qt6-tools-dev \
+  qt6-tools-dev-tools \
+  qt6-l10n-tools \
+  libqt6charts6-dev \
+  libqt6opengl6-dev \
+  libzip-dev \
+  mesa-common-dev \
+  libglu1-mesa-dev \
+  build-essential \
+  gnupg \
+  bc \
+  ninja-build \
+  apt-transport-https && \
+  wget -O /tmp/kitware-archive.key https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null && \
+  gpg --dearmor /tmp/kitware-archive.key && \
+  mv /tmp/kitware-archive.key.gpg /usr/share/keyrings/kitware-archive-keyring.gpg && \
+  echo "deb [signed-by=/usr/share/keyrings/kitware-archive-keyring.gpg] https://apt.kitware.com/ubuntu/ jammy main" > /etc/apt/sources.list.d/kitware.list && \
+  apt-get update && \
+  apt-get -y install cmake cmake-data && \
+  update-alternatives --install /usr/bin/qmake qmake /usr/lib/qt6/bin/qmake6 100 && \
+  apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+COPY . /opt/dsi-studio/src
+RUN cd /opt/dsi-studio \
+  && sed -i '/color_bar_dialog/d;/filebrowser/d;/mac_filesystem/d' src/dsi_studio.pro \
+  && sed -i 's/DSI_STUDIO_LOGIN/""/g' src/mainwindow.cpp \
+  && mkdir build && cd build \
+  && qmake ../src/dsi_studio.pro && make -j 1
+
+ARG ATLAS_SHA=59a1ca250845e569813ca6a2c5702d74f4d4cb4a
+ARG UNET_SHA=3ec6aa9513c0c8bbb90399a7af16245b594cd09b
+
+RUN cd /opt/dsi-studio \
+  && mv build/dsi_studio . \
+  && chmod 755 dsi_studio \
+  && cp -R src/other/* . \
+  && rm -rf src build \
+  && curl -sSLO https://github.com/frankyeh/UNet-Studio-Data/archive/${UNET_SHA}.zip \
+  && unzip ${UNET_SHA}.zip \
+  && rm ${UNET_SHA}.zip \
+  && mv UNet-Studio-Data-${UNET_SHA}/network/ . \
+  && rm -rf UNet-Studio-Data-${UNET_SHA} \
+  && curl -sSLO https://github.com/data-others/atlas/archive/${ATLAS_SHA}.zip \
+  && unzip ${ATLAS_SHA}.zip \
+  && rm -rf DSI-Studio-atlas-${ATLAS_SHA}/.git \
+  && mv atlas-${ATLAS_SHA} atlas \
+  && rm ${ATLAS_SHA}.zip

cmd/ana.cpp

@@ -673,7 +673,8 @@ int ana_tract(tipl::program_option<tipl::out>& po,std::shared_ptr<fib_data> hand
                 }
             }
             if(tipl::ends_with(output,".trk.gz") ||
-               tipl::ends_with(output,".tt.gz"))
+               tipl::ends_with(output,".tt.gz") ||
+               tipl::ends_with(output,".trx"))
             {
                 tipl::out() << "saving multiple tracts into one file: " << output;
                 if(!TractModel::save_all(output,tracts))

cmd/trk.cpp

@@ -487,7 +487,7 @@ int trk_post(tipl::program_option<tipl::out>& po,
 
     if(output_track)
     {
-        if(!tipl::ends_with(tract_file_name,{".tt.gz",".trk.gz",".trk",".tck",".txt",".mat"}))
+        if(!tipl::ends_with(tract_file_name,{".tt.gz",".trx",".trk.gz",".trk",".tck",".txt",".mat"}))
             tract_file_name += "." + po.get("trk_format","tt.gz");
         bool failed = false;
         if(po.has("ref")) // save track in T1W/T2W space

dsi_studio.pro

@@ -0,0 +1,191 @@
+QT += core \
+    gui \
+    opengl \
+    charts \
+    network
+
+greaterThan(QT_MAJOR_VERSION, 5): QT += widgets
+equals(QT_MAJOR_VERSION, 6): DEFINES += QT6_PATCH
+
+CONFIG += c++17
+# CONFIG += console
+
+TARGET = dsi_studio
+TEMPLATE = app
+
+INCLUDEPATH += ./plot
+DEFINES += TIPL_USE_QT
+
+linux* {
+QMAKE_CXXFLAGS += -fpermissive -Wno-sign-compare
+CONFIG += link_pkgconfig
+PKGCONFIG += libzip eigen3
+PKGCONFIG += spdlog fmt
+LIBS += -lGLU -lz -lzip -lspdlog -lfmt
+}
+
+win32* {
+INCLUDEPATH += ../include $$[QT_INSTALL_HEADERS]/QtZlib
+QMAKE_CXXFLAGS += -wd4244 -wd4267 -wd4018
+LIBS += -lOpenGL32 -lGlu32
+RC_ICONS = dsi_studio.ico
+}
+
+mac {
+QMAKE_MACOSX_DEPLOYMENT_TARGET = 10.15
+INCLUDEPATH += /Users/admin/include
+ICON = dsi_studio.icns
+LIBS += -lz
+}
+
+INCLUDEPATH += libs \
+    libs/dsi \
+    libs/tracking \
+    libs/mapping \
+    dicom \
+    /home/matt/projects/trx_dsi_studio/DSI-Studio-TRX/trx-cpp/include
+
+HEADERS += mainwindow.h \
+    console.h \
+    dicom/dicom_parser.h \
+    dicom/dwi_header.hpp \
+    libs/dsi/tessellated_icosahedron.hpp \
+    libs/dsi/odf_process.hpp \
+    libs/dsi/image_model.hpp \
+    libs/dsi/gqi_process.hpp \
+    libs/dsi/gqi_mni_reconstruction.hpp \
+    libs/dsi/dti_process.hpp \
+    libs/dsi/basic_voxel.hpp \
+    SliceModel.h \
+    tracking/tracking_window.h \
+    reconstruction/reconstruction_window.h \
+    tracking/slice_view_scene.h \
+    opengl/glwidget.h \
+    opengl/renderingtablewidget.h \
+    opengl/tract_render.hpp \
+    opengl/region_render.hpp \
+    libs/tracking/tracking_method.hpp \
+    libs/tracking/roi.hpp \
+    libs/tracking/fib_data.hpp \
+    libs/tracking/basic_process.hpp \
+    libs/tracking/tract_cluster.hpp \
+    tracking/region/regiontablewidget.h \
+    tracking/region/Regions.h \
+    libs/tracking/tract_model.hpp \
+    tracking/tract/tracttablewidget.h \
+    qcolorcombobox.h \
+    libs/tracking/tracking_thread.hpp \
+    libs/mapping/atlas.hpp \
+    view_image.h \
+    manual_alignment.h \
+    tracking/tract_report.hpp \
+    tracking/connectivity_matrix_dialog.h \
+    tracking/atlasdialog.h \
+    qcompletelineedit.h \
+    libs/mapping/connectometry_db.hpp \
+    connectometry/createdbdialog.h \
+    connectometry/match_db.h \
+    connectometry/db_window.h \
+    connectometry/group_connectometry.hpp \
+    connectometry/group_connectometry_analysis.h \
+    regtoolbox.h \
+    auto_track.h \
+    tracking/device.h \
+    tracking/devicetablewidget.h \
+    libs/dsi/hist_process.hpp \
+    xnat_dialog.h \
+    /home/matt/projects/trx_dsi_studio/DSI-Studio-TRX/trx-cpp/include/trx/trx.h \
+    /home/matt/projects/trx_dsi_studio/DSI-Studio-TRX/trx-cpp/include/trx/trx.tpp \
+    /home/matt/projects/trx_dsi_studio/DSI-Studio-TRX/trx-cpp/include/trx/filesystem.h
+
+FORMS += mainwindow.ui \
+    console.ui \
+    tracking/tracking_window.ui \
+    reconstruction/reconstruction_window.ui \
+    dicom/dicom_parser.ui \
+    view_image.ui \
+    manual_alignment.ui \
+    tracking/tract_report.ui \
+    tracking/connectivity_matrix_dialog.ui \
+    tracking/atlasdialog.ui \
+    connectometry/createdbdialog.ui \
+    connectometry/match_db.ui \
+    connectometry/db_window.ui \
+    connectometry/group_connectometry.ui \
+    regtoolbox.ui \
+    auto_track.ui \
+    xnat_dialog.ui
+
+RESOURCES += \
+    icons.qrc
+
+SOURCES += main.cpp \
+    console.cpp \
+    mainwindow.cpp \
+    dicom/dicom_parser.cpp \
+    dicom/dwi_header.cpp \
+    cmd/img.cpp \
+    libs/dsi/dsi_interface_imp.cpp \
+    libs/dsi/gqi_process.cpp \
+    libs/tracking/tract_cluster.cpp \
+    SliceModel.cpp \
+    tracking/tracking_window.cpp \
+    tracking/tracking_window_action.cpp \
+    reconstruction/reconstruction_window.cpp \
+    tracking/slice_view_scene.cpp \
+    opengl/glwidget.cpp \
+    opengl/tract_render.cpp \
+    opengl/region_render.cpp \
+    opengl/renderingtablewidget.cpp \
+    tracking/region/regiontablewidget.cpp \
+    tracking/region/Regions.cpp \
+    libs/tracking/tract_model.cpp \
+    tracking/tract/tracttablewidget.cpp \
+    qcolorcombobox.cpp \
+    cmd/trk.cpp \
+    cmd/rec.cpp \
+    cmd/src.cpp \
+    libs/mapping/atlas.cpp \
+    cmd/ana.cpp \
+    view_image.cpp \
+    manual_alignment.cpp \
+    tracking/tract_report.cpp \
+    cmd/exp.cpp \
+    tracking/connectivity_matrix_dialog.cpp \
+    libs/dsi/tessellated_icosahedron.cpp \
+    cmd/atl.cpp \
+    tracking/atlasdialog.cpp \
+    cmd/cnt.cpp \
+    cmd/vis.cpp \
+    qcompletelineedit.cpp \
+    libs/tracking/roi.cpp \
+    libs/tracking/fib_data.cpp \
+    libs/tracking/tracking_thread.cpp \
+    cmd/ren.cpp \
+    libs/mapping/connectometry_db.cpp \
+    connectometry/createdbdialog.cpp \
+    connectometry/match_db.cpp \
+    connectometry/db_window.cpp \
+    connectometry/group_connectometry.cpp \
+    connectometry/group_connectometry_analysis.cpp \
+    regtoolbox.cpp \
+    cmd/cnn.cpp \
+    cmd/qc.cpp \
+    libs/dsi/basic_voxel.cpp \
+    libs/dsi/image_model.cpp \
+    cmd/reg.cpp \
+    auto_track.cpp \
+    cmd/atk.cpp \
+    tracking/device.cpp \
+    tracking/devicetablewidget.cpp \
+    cmd/xnat.cpp \
+    xnat_dialog.cpp \
+    /home/matt/projects/trx_dsi_studio/DSI-Studio-TRX/trx-cpp/src/trx.cpp
+
+OTHER_FILES += \
+    options.txt \
+    dicom_tag.txt \
+    FreeSurferColorLUT.txt
+
+DISTFILES += \
+    LICENSE