Feature/dicom reader

README.md

@@ -1,6 +1,8 @@
 # AGAVE : Advanced GPU Accelerated Volume Explorer
 
-AGAVE is a desktop application for viewing multichannel volume data. Several formats are supported, including OME-ZARR 0.4 and 0.5, OME-TIFF and Zeiss .czi files.
+AGAVE is a desktop application for viewing multichannel volume data. Several formats are supported, including OME-ZARR 0.4 and 0.5, OME-TIFF, Zeiss .czi, and grayscale DICOM files (.dcm, .dicom, .ima).
+
+The DICOM reader uses DCMTK 3.7.0. It opens single 8-bit or 16-bit grayscale DICOM objects and folders of DICOM slices, including nested study/series folders. Each `SeriesInstanceUID` is a selectable scene. Slices are ordered by image position and orientation, then by instance number or filename when spatial metadata is absent; irregular stacks are rejected. Multi-frame objects become Z stacks. The reader decodes uncompressed, RLE, JPEG, and JPEG-LS transfer syntaxes supported by DCMTK and maps displayed intensity into Agave's unsigned 16-bit volume format. Color images and JPEG 2000 are not yet supported.
 
 ![screenshot](https://github.com/user-attachments/assets/b96618f2-7020-4b93-936e-9b32b795ea83)
 

agave_app/agaveGui.cpp

@@ -223,7 +223,7 @@ agaveGui::createActions()
   m_openUrlAction->setStatusTip(tr("Open an existing volume in the cloud"));
   connect(m_openUrlAction, SIGNAL(triggered()), this, SLOT(openUrl()));
 
-  m_openDirectoryAction = new QAction(tr("&Open directory (.zarr)"), this);
+  m_openDirectoryAction = new QAction(tr("&Open directory (.zarr, DICOM)"), this);
   m_openDirectoryAction->setShortcuts(QKeySequence::Open);
   m_openDirectoryAction->setStatusTip(tr("Open an existing volume from local directory"));
   connect(m_openDirectoryAction, SIGNAL(triggered()), this, SLOT(openDirectory()));

renderlib/io/CMakeLists.txt

@@ -15,6 +15,8 @@ target_sources(renderlib PRIVATE
 "${CMAKE_CURRENT_SOURCE_DIR}/FileReaderCCP4.h"
 "${CMAKE_CURRENT_SOURCE_DIR}/FileReaderCzi.cpp"
 "${CMAKE_CURRENT_SOURCE_DIR}/FileReaderCzi.h"
+"${CMAKE_CURRENT_SOURCE_DIR}/FileReaderDicom.cpp"
+"${CMAKE_CURRENT_SOURCE_DIR}/FileReaderDicom.h"
 "${CMAKE_CURRENT_SOURCE_DIR}/FileReaderImageSequence.cpp"
 "${CMAKE_CURRENT_SOURCE_DIR}/FileReaderImageSequence.h"
 "${CMAKE_CURRENT_SOURCE_DIR}/FileReaderTIFF.cpp"
@@ -41,6 +43,26 @@ add_subdirectory(libCZI)
 
 # end libczi dependency
 
+# Build only the DCMTK modules needed for grayscale image decoding.  The JPEG
+# and JPEG-LS modules also link to dcmimage, even for grayscale images.
+set(DCMTK_MODULES "ofstd;oflog;oficonv;dcmdata;dcmimgle;dcmimage;dcmjpeg;dcmjpls" CACHE STRING "DCMTK modules" FORCE)
+set(DCMTK_DEFAULT_DICT builtin CACHE STRING "Embed the DCMTK dictionary for standalone Agave builds" FORCE)
+set(BUILD_APPS OFF CACHE BOOL "Build DCMTK command line applications" FORCE)
+set(DCMTK_WITH_OPENSSL OFF CACHE BOOL "DCMTK TLS support" FORCE)
+set(DCMTK_WITH_ICONV OFF CACHE BOOL "DCMTK iconv support" FORCE)
+set(DCMTK_WITH_ICU OFF CACHE BOOL "DCMTK ICU support" FORCE)
+set(DCMTK_WITH_PNG OFF CACHE BOOL "DCMTK PNG support" FORCE)
+set(DCMTK_WITH_TIFF OFF CACHE BOOL "DCMTK TIFF support" FORCE)
+set(DCMTK_WITH_XML OFF CACHE BOOL "DCMTK XML support" FORCE)
+set(DCMTK_WITH_OPENJPEG OFF CACHE BOOL "DCMTK JPEG 2000 support" FORCE)
+set(DCMTK_WITH_DOXYGEN OFF CACHE BOOL "DCMTK API documentation" FORCE)
+FetchContent_Declare(
+  dcmtk
+  URL "https://github.com/DCMTK/dcmtk/archive/refs/tags/DCMTK-3.7.0.tar.gz"
+  URL_HASH SHA256=5bb3ec8317dc465788bed2ca789e76d03ae5848c9381cce3b14c1a3f8b6aca56
+)
+FetchContent_MakeAvailable(dcmtk)
+
 # Use these system/vcpkg-provided dependencies instead of tensorstore's bundled ones.
 set(TENSORSTORE_USE_SYSTEM_TIFF ON)
 set(TENSORSTORE_USE_SYSTEM_ZLIB ON)
@@ -56,7 +78,7 @@ FetchContent_MakeAvailable(tensorstore)
 
 target_link_libraries(renderlib
 libCZI
+ dcmdata dcmimgle dcmimage dcmjpeg dcmjpls
 
 tensorstore::tensorstore tensorstore::all_drivers
 )
-

renderlib/io/FileReader.cpp

@@ -2,6 +2,7 @@
 
 #include "FileReaderCCP4.h"
 #include "FileReaderCzi.h"
+#include "FileReaderDicom.h"
 #include "FileReaderImageSequence.h"
 #include "FileReaderTIFF.h"
 #include "FileReaderTestVolume.h"
@@ -54,16 +55,22 @@ FileReader::getReader(const std::string& filepath, bool isImageSequence)
     return new FileReaderTIFF(filepath);
   } else if (extstr == ".czi") {
     return new FileReaderCzi(filepath);
+  } else if (extstr == ".dcm" || extstr == ".dicom" || extstr == ".ima") {
+    return new FileReaderDicom(filepath);
   } else if (extstr == ".map" || extstr == ".mrc") {
     return new FileReaderCCP4(filepath);
   } else if (extstr == ".zarr") {
     return new FileReaderZarr(filepath);
   }
-  // if it's a directory, and contains the string zarr anywhere, we assume it's a zarr
+  // A directory with Zarr metadata is a Zarr store; other directories can
+  // contain DICOM series, including files without a DICOM extension.
   else if (std::filesystem::is_directory(filepath)) {
-    if (filepath.find("zarr") != std::string::npos) {
+    const std::filesystem::path directory(filepath);
+    if (std::filesystem::exists(directory / "zarr.json") || std::filesystem::exists(directory / ".zgroup") ||
+        std::filesystem::exists(directory / ".zarray") || std::filesystem::exists(directory / ".zattrs")) {
       return new FileReaderZarr(filepath);
     }
+    return new FileReaderDicom(filepath);
   }
 
   return nullptr;