BF: make fslcomplex preserve image orientation

This MR fixes fslcomplex so that output files have the same orientation information as (complex) input files. The read_complexvolume function reads in a complex64 image as separate real/imaginary volume<float> objects, but was only performing a L/R flip, and was not actually setting header information in the loaded volumes.

Fixes avwutils#5 (closed)

generalio.cc

@@ -576,11 +576,16 @@ int read_complexvolume(volume<float>& realvols, volume<float>& imagvols,
       extensions.clear();
     }
 
-    for ( size_t voxel=0;voxel<volsize && !isComplex;voxel++) //Only copy real buffer for non-complex
-      rbuffer[voxel]=((float*)buffer)[voxel];
-    for ( size_t voxel=0;voxel<volsize && isComplex;voxel++) {
-      rbuffer[voxel]=((float *)buffer)[2*voxel];
-    ibuffer[voxel]=((float *)buffer)[2*voxel+1];
+    //Only copy real buffer for non-complex
+    if (!isComplex) {
+      for ( size_t voxel=0;voxel<volsize && !isComplex;voxel++)
+        rbuffer[voxel]=((float*)buffer)[voxel];
+    }
+    else {
+      for ( size_t voxel=0;voxel<volsize && isComplex;voxel++) {
+        rbuffer[voxel]=((float *)buffer)[2*voxel];
+        ibuffer[voxel]=((float *)buffer)[2*voxel+1];
+      }
     }
     realvols.reinitialize(sx,sy,sz,st,rbuffer,true);
     imagvols.reinitialize(sx,sy,sz,st,ibuffer,true);
@@ -588,16 +593,10 @@ int read_complexvolume(volume<float>& realvols, volume<float>& imagvols,
 
   realvols.setdims(niihdr.pixdim[1],niihdr.pixdim[2],niihdr.pixdim[3],niihdr.pixdim[4]);
   imagvols.setdims(niihdr.pixdim[1],niihdr.pixdim[2],niihdr.pixdim[3],niihdr.pixdim[4]);
-  // swap to Radiological when necessary
-  if ( NiftiGetLeftRightOrder(niihdr) != FSL_RADIOLOGICAL ) {
-    realvols.RadiologicalFile = false;
-    realvols.makeradiological();
-    imagvols.RadiologicalFile = false;
-    imagvols.makeradiological();
-  } else {
-    realvols.RadiologicalFile = true;
-    imagvols.RadiologicalFile = true;
-  }
+
+  set_volume_properties(niihdr,realvols);
+  set_volume_properties(niihdr,imagvols);
+
   delete [] buffer;
   return 0;
 }