partial commit - use STIR's ITKImageInputFileFormat for offset

src/Synergistic/tests/test_cSynergistic.cpp

@@ -58,26 +58,26 @@ int main(int argc, char* argv[])
         if (argc==1) SIRF_PATH = getenv("SIRF_PATH");
         else         SIRF_PATH = argv[1];
 
-        // Test STIR -> Nifti
+        // Test Nifti -> STIR -> Nifti
             {
             // Input filenames
             const std::string nifti_filename = SIRF_PATH + "/data/examples/Registration/test2.nii.gz";
 
             // Load the image as a NiftiImageData3D
             NiftiImageData3D<float> image_nifti(nifti_filename);
 
-            // Read as STIRImageData, convert NiftiImageData3D and save to file
-            STIRImageData image_stir(nifti_filename);
-            NiftiImageData3D<float> image_nifti_from_stir(image_stir);
-            image_nifti_from_stir.write("results/stir_to_nifti.nii",image_nifti.get_original_datatype());
+            // Convert to STIR and save to file
+            STIRImageData image_nifti_to_stir(image_nifti);
+            const std::string output_file_format = "results/stir_output_file_format_nifti.par";
+            create_stir_output_file_format(output_file_format);
+            image_nifti_to_stir.write("results/nifti_to_stir.nii",output_file_format);
 
-            // Compare the two
-            if (image_nifti != image_nifti_from_stir)
-                throw std::runtime_error("Conversion from STIR to Nifti failed");
+            // Convert back to Nifti, save and compare
+            NiftiImageData3D<float> image_nifti_to_stir_to_nifti(image_nifti_to_stir);
+            image_nifti_to_stir_to_nifti.write("results/nifti_to_stir_to_nifti.nii",image_nifti.get_original_datatype());
 
-            // Also save the STIRImageData to file (might be useful visual for comparison)
-            create_stir_output_file_format("results/stir_output_file_format_nifti.par");
-            image_stir.write("results/stir.nii","results/stir_output_file_format_nifti.par");
+            if (image_nifti != image_nifti_to_stir_to_nifti)
+                throw std::runtime_error("Conversion Nifti->STIR->Nifti failed");
         }
 
         // Test Gadgetron -> Nifti

src/xSTIR/cSTIR/stir_data_containers.cpp

@@ -248,27 +248,31 @@ const DataContainer& a_y
 
 STIRImageData::STIRImageData(const ImageData& id)
 {
-    throw std::runtime_error("TODO - create STIRImageData from general SIRFImageData.");
-    /* The following is incorrect.
-    Dimensions dim = id.dimensions();
-    int nx = dim["x"];
-    int ny = dim["y"];
-    int nz = 1;
-    Dimensions::iterator it = dim.begin();
-    while (it != dim.end()) {
-        if (it->first != "x" && it->first != "y")
-            nz *= it->second;
-        ++it;
-    }
-    Voxels3DF voxels(stir::IndexRange3D(0, nz - 1,
-        -(ny / 2), -(ny / 2) + ny - 1, -(nx / 2), -(nx / 2) + nx - 1),
-        Coord3DF(0, 0, 0),
-        Coord3DF(3, 3, 3.375));
-    _data.reset(voxels.clone());
-    copy(id.begin(), begin(), end());
+    // Get range from number of voxels
+    const VoxelisedGeometricalInfo3D::Size &sz =
+            id.get_geom_info_sptr()->get_size();
+    stir::IndexRange3D range(0, sz[2] - 1,
+            -(sz[1] / 2), -(sz[1] / 2) + sz[1] - 1,
+            -(sz[0] / 2), -(sz[0] / 2) + sz[0] - 1);
+
+    // Spacing (STIR is z,y,x)
+    const VoxelisedGeometricalInfo3D::Spacing &sp =
+            id.get_geom_info_sptr()->get_spacing();
+    Coord3DF spacing(sp[2], sp[1], sp[0]);
+
+    // Offset
+    const VoxelisedGeometricalInfo3D::Offset &of =
+            id.get_geom_info_sptr()->get_offset();
+    Coord3DF offset(of[2], of[1], of[0]);
+
+    // Construct image
+    this->_data = std::make_shared<Voxels3DF>(range,offset,spacing);
+
+    // Copy voxel values
+    this->ImageData::fill(id);
 
     // Set up the geom info
-    this->set_up_geom_info();*/
+    this->set_up_geom_info();
 }
 
 void