Feat/nifti support

CMakeLists.txt

@@ -22,15 +22,17 @@ if(NOT CMAKE_BUILD_TYPE)
 endif()
 
 set(CMAKE_CXX_FLAGS_RELEASE "-O2")
-set(SOURCE 
+set(SOURCE
           src/cpp/ts_driver/tiled_tiff/omexml.cc
           src/cpp/ts_driver/tiled_tiff/tiled_tiff_key_value_store.cc
           src/cpp/ts_driver/ometiff/metadata.cc
           src/cpp/ts_driver/ometiff/driver.cc
           src/cpp/interface/interface.cpp
           src/cpp/reader/tsreader.cpp
+          src/cpp/reader/niftireader.cpp
           src/cpp/utilities/utilities.cpp
           src/cpp/writer/tswriter.cpp
+          src/cpp/writer/niftiwriter.cpp
 )
 
 include(FetchContent)
@@ -61,6 +63,9 @@ else ()
 	message(STATUS "Unable to find threads. bfio_cpp must have a threading library i.e. pthreads.")
 endif ()
 
+#==== ZLIB (system, required for NIfTI .nii.gz decompression)
+find_package(ZLIB REQUIRED)
+
 #==== Pybind11
 find_package(pybind11 CONFIG REQUIRED)
 
@@ -76,7 +81,8 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
     target_link_libraries(libbfiocpp PRIVATE stdc++fs)
 endif()
 
-target_link_libraries(libbfiocpp PRIVATE 
-                      tensorstore::tensorstore 
-                      tensorstore::all_drivers)
+target_link_libraries(libbfiocpp PRIVATE
+                      tensorstore::tensorstore
+                      tensorstore::all_drivers
+                      ZLIB::ZLIB)
 target_link_libraries(libbfiocpp PRIVATE ${Build_LIBRARIES})  

README.md

@@ -1,5 +1,14 @@
 This is the new backend for `bfio`, using `Tensorstore` and other high-throughput IO library
 
+## Supported Formats
+
+| Format | Read | Write |
+|--------|------|-------|
+| OME-TIFF | Yes | No |
+| OME-Zarr v2 | Yes | Yes |
+| OME-Zarr v3 | Yes | Yes |
+| NIfTI (.nii, .nii.gz) | Yes | Yes |
+
 ## Build Requirements
 
 `bfiocpp` uses `Tensorstore` for reading and writing OME Tiff and OME Zarr files. So `Tensorstore` build requirements are needed to be satisfied for `bfiocpp` also. 

ci-utils/install_prereq_linux.sh

@@ -13,46 +13,54 @@ fi
 
 mkdir -p $LOCAL_INSTALL_DIR
 
+# Set CMAKE_INSTALL_PREFIX to /usr/local when running in GitHub Actions,
+# otherwise install into LOCAL_INSTALL_DIR.
+if [ -n "$SYS_INSTALL" ]; then
+    DEPS_INSTALL_PREFIX="/usr/local"
+else
+    DEPS_INSTALL_PREFIX="$PWD/$LOCAL_INSTALL_DIR"
+fi
+
+
+
 curl -L https://github.com/pybind/pybind11/archive/refs/tags/v2.12.0.zip -o v2.12.0.zip
-unzip v2.12.0.zip
+unzip -o v2.12.0.zip
 cd pybind11-2.12.0
-mkdir build_man
+mkdir -p build_man
 cd build_man
-cmake -DCMAKE_INSTALL_PREFIX=../../$LOCAL_INSTALL_DIR/  -DPYBIND11_TEST=OFF ..
+cmake -DCMAKE_INSTALL_PREFIX="$DEPS_INSTALL_PREFIX" -DPYBIND11_TEST=OFF ..
 make install -j4
 cd ../../
 
 
 curl -L https://github.com/madler/zlib/releases/download/v1.3.1/zlib131.zip -o zlib131.zip
-unzip zlib131.zip
+unzip -o zlib131.zip
 cd zlib-1.3.1
-mkdir build_man
+mkdir -p build_man
 cd build_man
-cmake -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DCMAKE_INSTALL_PREFIX=/usr/local ..  
-cmake --build . 
+cmake -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DCMAKE_INSTALL_PREFIX="$DEPS_INSTALL_PREFIX" ..
+cmake --build .
 cmake --build . --target install 
 cd ../../
 
 curl -L https://github.com/libjpeg-turbo/libjpeg-turbo/archive/refs/tags/3.1.0.zip -o 3.1.0.zip
-unzip 3.1.0.zip
+unzip -o 3.1.0.zip
 cd libjpeg-turbo-3.1.0
-mkdir build_man
+mkdir -p build_man
 cd build_man
-cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DENABLE_STATIC=FALSE -DCMAKE_BUILD_TYPE=Release ..
+cmake -DCMAKE_INSTALL_PREFIX="$DEPS_INSTALL_PREFIX" -DENABLE_STATIC=FALSE -DCMAKE_BUILD_TYPE=Release ..
 if [[ "$OSTYPE" == "darwin"* ]]; then
   sudo make install -j4
 else
   make install -j4
 fi
 cd ../../
-make install -j4
-cd ../../
 
 curl -L  https://github.com/glennrp/libpng/archive/refs/tags/v1.6.53.zip -o v1.6.53.zip
-unzip v1.6.53.zip
+unzip -o v1.6.53.zip
 cd libpng-1.6.53
-mkdir build_man
+mkdir -p build_man
 cd build_man
-cmake -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DCMAKE_INSTALL_PREFIX=/usr/local ..
+cmake -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DCMAKE_INSTALL_PREFIX="$DEPS_INSTALL_PREFIX" ..
 make install -j4
 cd ../../

src/cpp/interface/interface.cpp

@@ -4,9 +4,11 @@
 #include <pybind11/numpy.h>
 #include <tuple>
 #include "../reader/tsreader.h"
+#include "../reader/niftireader.h"
 #include "../utilities/sequence.h"
 #include "../utilities/utilities.h"
 #include "../writer/tswriter.h"
+#include "../writer/niftiwriter.h"
 
 namespace py = pybind11;
 using bfiocpp::Seq;
@@ -69,6 +71,19 @@ py::array get_iterator_requested_tile_data(bfiocpp::TsReaderCPP& tl,  std::int64
     return as_pyarray_shared_5d(tmp, ih, iw, id, nc, nt) ;
 }
 
+py::array get_nifti_image_data(bfiocpp::NiftiReaderCPP& nr,
+                               const Seq& rows, const Seq& cols,
+                               const Seq& layers, const Seq& channels,
+                               const Seq& tsteps) {
+    auto tmp = nr.GetImageData(rows, cols, layers, channels, tsteps);
+    auto ih = rows.Stop()    - rows.Start()    + 1;
+    auto iw = cols.Stop()    - cols.Start()    + 1;
+    auto id = layers.Stop()  - layers.Start()  + 1;
+    auto nc = channels.Stop()- channels.Start()+ 1;
+    auto nt = tsteps.Stop()  - tsteps.Start()  + 1;
+    return as_pyarray_shared_5d(tmp, ih, iw, id, nc, nt);
+}
+
 PYBIND11_MODULE(libbfiocpp, m) {
     py::class_<Seq, std::shared_ptr<Seq>>(m, "Seq")  
         .def(py::init<const size_t, const size_t, const size_t>());
@@ -116,12 +131,44 @@ PYBIND11_MODULE(libbfiocpp, m) {
         .value("OmeTiff", bfiocpp::FileType::OmeTiff)
         .value("OmeZarrV2", bfiocpp::FileType::OmeZarrV2)
         .value("OmeZarrV3", bfiocpp::FileType::OmeZarrV3)
+        .value("Nifti", bfiocpp::FileType::Nifti)
+        .value("NiftiGz", bfiocpp::FileType::NiftiGz)
         .export_values();
+
+    py::class_<bfiocpp::NiftiReaderCPP, std::shared_ptr<bfiocpp::NiftiReaderCPP>>(m, "NiftiReaderCPP")
+    .def(py::init<const std::string&>())
+    .def("get_image_height",  &bfiocpp::NiftiReaderCPP::GetImageHeight)
+    .def("get_image_width",   &bfiocpp::NiftiReaderCPP::GetImageWidth)
+    .def("get_image_depth",   &bfiocpp::NiftiReaderCPP::GetImageDepth)
+    .def("get_tile_height",   &bfiocpp::NiftiReaderCPP::GetTileHeight)
+    .def("get_tile_width",    &bfiocpp::NiftiReaderCPP::GetTileWidth)
+    .def("get_tile_depth",    &bfiocpp::NiftiReaderCPP::GetTileDepth)
+    .def("get_channel_count", &bfiocpp::NiftiReaderCPP::GetChannelCount)
+    .def("get_tstep_count",   &bfiocpp::NiftiReaderCPP::GetTstepCount)
+    .def("get_datatype",      &bfiocpp::NiftiReaderCPP::GetDataType)
+    .def("get_physical_size_x", &bfiocpp::NiftiReaderCPP::GetPhysicalSizeX)
+    .def("get_physical_size_y", &bfiocpp::NiftiReaderCPP::GetPhysicalSizeY)
+    .def("get_physical_size_z", &bfiocpp::NiftiReaderCPP::GetPhysicalSizeZ)
+    .def("get_image_data",
+        [](bfiocpp::NiftiReaderCPP& nr, const Seq& rows, const Seq& cols,
+           const Seq& layers, const Seq& channels, const Seq& tsteps) {
+            return get_nifti_image_data(nr, rows, cols, layers, channels, tsteps);
+        }, py::return_value_policy::reference);
 
     m.def("get_ome_xml", &bfiocpp::GetOmeXml);
 
-
-    // Writer class
+    // NIfTI writer
+    py::class_<bfiocpp::NiftiWriterCPP, std::shared_ptr<bfiocpp::NiftiWriterCPP>>(m, "NiftiWriterCPP")
+    .def(py::init<const std::string&, const std::vector<std::int64_t>&,
+                  const std::string&, const std::string&>(),
+         py::arg("filename"),
+         py::arg("image_shape"),
+         py::arg("dtype"),
+         py::arg("dimension_order"))
+    .def("write_image_data", &bfiocpp::NiftiWriterCPP::WriteImageData)
+    .def("close", &bfiocpp::NiftiWriterCPP::Close);
+
+    // Zarr/OME-TIFF writer
     py::class_<bfiocpp::TsWriterCPP, std::shared_ptr<bfiocpp::TsWriterCPP>>(m, "TsWriterCPP")
     .def(py::init<const std::string&, const std::vector<std::int64_t>&, const std::vector<std::int64_t>&, const std::string&, const std::string&, bfiocpp::FileType>(),
          py::arg("filename"),