Merge pull request #103 from sameeul/binary_segmentation

read binary segmentation image
PolusAI · May 1, 2023 · cba754a · cba754a
2 parents 967cef3 + 1ec7f47
commit cba754a
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Showing 3 changed files with 46 additions and 4 deletions.
diff --git a/ci-utils/install_prereq_linux.sh b/ci-utils/install_prereq_linux.sh
@@ -149,7 +149,7 @@ unzip v2.5.0.zip
 cd openjpeg-2.5.0/
 mkdir build_man
 cd build_man/
-cmake -DCMAKE_INSTALL_PREFIX=../../$Z5_INSTALL_DIR/   -DCMAKE_PREFIX_PATH=../../$Z5_INSTALL_DIR/   ..
+cmake -DCMAKE_INSTALL_PREFIX=../../$Z5_INSTALL_DIR/   -DCMAKE_PREFIX_PATH=../../$Z5_INSTALL_DIR/ -DBUILD_CODEC=OFF   ..
 make install -j4
 cd ../../
 
@@ -158,6 +158,6 @@ unzip DCMTK-3.6.7.zip
 cd dcmtk-DCMTK-3.6.7/
 mkdir build_man
 cd build_man/
-cmake -DCMAKE_INSTALL_PREFIX=../../$Z5_INSTALL_DIR/   -DCMAKE_PREFIX_PATH=../../$Z5_INSTALL_DIR/  -DDCMTK_WITH_ICONV=OFF -DBUILD_SHARED_LIBS=ON  ..
+cmake -DCMAKE_INSTALL_PREFIX=../../$Z5_INSTALL_DIR/   -DCMAKE_PREFIX_PATH=../../$Z5_INSTALL_DIR/  -DDCMTK_WITH_ICONV=OFF -DBUILD_SHARED_LIBS=ON -DBUILD_APPS=OFF  ..
 make install -j4
 cd ../../
diff --git a/ci-utils/install_prereq_win.bat b/ci-utils/install_prereq_win.bat
@@ -132,7 +132,7 @@ tar -xvf v2.5.0.zip
 pushd openjpeg-2.5.0
 mkdir build_man
 pushd build_man
-cmake -DCMAKE_INSTALL_PREFIX=../../local_install/   -DCMAKE_PREFIX_PATH=../../local_install/   ..
+cmake -DCMAKE_INSTALL_PREFIX=../../local_install/   -DCMAKE_PREFIX_PATH=../../local_install/  -DBUILD_CODEC=OFF  ..
 cmake --build . --config Release --target install --parallel 4
 popd
 popd
@@ -147,7 +147,7 @@ tar -xvf DCMTK-3.6.7.zip
 pushd dcmtk-DCMTK-3.6.7
 mkdir build_man
 pushd build_man
-cmake -DCMAKE_INSTALL_PREFIX=../../local_install/ -DCMAKE_PREFIX_PATH=../../local_install/ -DBUILD_SHARED_LIBS=ON -DDCMTK_WITH_ICONV=OFF -DDCMTK_WITH_TIFF=ON -DWITH_LIBTIFFINC=../../local_install -DDCMTK_WITH_PNG=ON -DWITH_LIBPNGINC=../../local_install -DDCMTK_WITH_ZLIB=ON -DWITH_ZLIBINC=../../local_install -DDCMTK_WITH_OPENJPEG=ON -DWITH_OPENJPEGINC=../../local_install ..
+cmake -DCMAKE_INSTALL_PREFIX=../../local_install/ -DCMAKE_PREFIX_PATH=../../local_install/ -DBUILD_SHARED_LIBS=ON -DDCMTK_WITH_ICONV=OFF -DDCMTK_WITH_TIFF=ON -DWITH_LIBTIFFINC=../../local_install -DDCMTK_WITH_PNG=ON -DWITH_LIBPNGINC=../../local_install -DDCMTK_WITH_ZLIB=ON -DWITH_ZLIBINC=../../local_install -DDCMTK_WITH_OPENJPEG=ON -DWITH_OPENJPEGINC=../../local_install  -DBUILD_APPS=OFF ..
 cmake --build . --config Release --target install --parallel 4
 popd
 popd

diff --git a/src/nyx/nyxus_dicom_loader.h b/src/nyx/nyxus_dicom_loader.h
@@ -6,6 +6,9 @@
 #include "dcmtk/dcmjpls/djdecode.h"  /* for JPEG-LS decoders */
 #include "dcmtk/dcmdata/dcrledrg.h"  /* for RLE decoder */
 #include "dcmtk/dcmjpeg/dipijpeg.h"  /* for dcmimage JPEG plugin */
+#include "dcmtk/dcmseg/segdoc.h"
+#include "dcmtk/dcmseg/segment.h"
+#include "dcmtk/dcmseg/segutils.h"
 
 template<class DataType>
 class NyxusGrayscaleDicomLoader : public AbstractTileLoader<DataType> 
@@ -141,6 +144,9 @@ class NyxusGrayscaleDicomLoader : public AbstractTileLoader<DataType>
             }       
         } else {
             switch(bitsPerSample_){
+                case 1:
+                    copyBinaryFrame(*tile, frame_no);
+                    break;
                 case 8:
                     copyFrame<uint8_t>(*tile, frame_no);
                     break;
@@ -249,6 +255,42 @@ class NyxusGrayscaleDicomLoader : public AbstractTileLoader<DataType>
 
     }
 
+    /// @brief Private function to copy and cast the values for Binary Segmentation Image
+    /// @tparam FileType Type inside the file
+    /// @param dest_as_vector Feature extraction facing buffer to fill
+    /// @param frame_no Frame to copy
+    void copyBinaryFrame(
+        std::vector<DataType>& dest_as_vector,
+        uint32_t frame_no) 
+    {   
+        DcmDataset* ds = dcm_ff_.getDataset();
+        DcmSegmentation *segdoc = nullptr;
+
+        OFCondition status = DcmSegmentation::loadDataset(*ds, segdoc);
+        if(status.good()){
+            const DcmIODTypes::Frame *frame = segdoc->getFrame(static_cast<size_t>(frame_no));
+            const DcmIODTypes::Frame *unpacked_frame = nullptr;
+            unpacked_frame = DcmSegUtils::unpackBinaryFrame(frame, tileHeight_, tileWidth_);
+            if(unpacked_frame){
+                if(dest_as_vector.size() < unpacked_frame->length){
+                    std::stringstream message;
+                    message
+                        << "Tile Loader ERROR: The destination buffer size ("
+                        <<dest_as_vector.size()
+                        <<") is smaller than the frame size ("
+                        << unpacked_frame->length <<").";
+                    throw (std::runtime_error(message.str()));
+                }
+                DataType* dest = dest_as_vector.data();
+                for(size_t i=0;i<unpacked_frame->length;++i){
+                    *(dest+i) = static_cast<DataType>(unpacked_frame->pixData[i]);
+                }
+                delete unpacked_frame;
+            }
+        }
+
+    }
+
     DcmFileFormat dcm_ff_;
     size_t
         fullHeight_ = 0,          ///< Full height in pixel