Add Header::ndim() assignment proxy

As discussed on MRtrix3#697.

cmd/5tt2gmwmi.cpp

@@ -146,7 +146,7 @@ void run ()
     H.datatype().set_byte_order_native();
   } else {
     H = input;
-    H.set_ndim (3);
+    H.ndim() = 3;
   }
   auto output = Image<float>::create (argument[1], H);
 

cmd/5tt2vis.cpp

@@ -85,7 +85,7 @@ void run ()
   DWI::Tractography::ACT::verify_5TT_image (input);
 
   Header H (input);
-  H.set_ndim (3);
+  H.ndim() = 3;
 
   const float bg_multiplier   = get_option_value ("bg",   VALUE_DEFAULT_BG);
   const float cgm_multiplier  = get_option_value ("cgm",  VALUE_DEFAULT_CGM);

cmd/dwi2adc.cpp

@@ -99,7 +99,7 @@ void run () {
 
   Header header (dwi);
   header.datatype() = DataType::Float32;
-  header.set_ndim (4);
+  header.ndim() = 4;
   header.size(3) = 2;
 
   auto adc = Image<value_type>::create (argument[1], header);

cmd/dwi2fod.cpp

@@ -223,7 +223,7 @@ void run ()
 
   auto header_in = Header::open (argument[1]);
   Header header_out (header_in);
-  header_out.set_ndim (4);
+  header_out.ndim() = 4;
   header_out.datatype() = DataType::Float32;
   header_out.datatype().set_byte_order_native();
   Stride::set_from_command_line (header_out, Stride::contiguous_along_axis (3, header_in));

cmd/dwi2noise.cpp

@@ -71,7 +71,7 @@ void run ()
   auto dwi_in = Image<value_type>::open (argument[0]);
 
   auto header = Header (dwi_in);
-  header.set_ndim (3);
+  header.ndim() = 3;
   header.datatype() = DataType::Float32;
   auto noise = Image<value_type>::create (argument[1], header);
 

cmd/dwi2tensor.cpp

@@ -180,7 +180,7 @@ void run ()
 
   Header header (dwi);
   header.datatype() = DataType::Float32;
-  header.set_ndim (4);
+  header.ndim() = 4;
 
   Image<value_type>* predict = nullptr;
   opt = get_options ("predicted_signal");
@@ -194,14 +194,14 @@ void run ()
   Image<value_type>* b0 = nullptr;
   opt = get_options ("b0");
   if (opt.size()) {
-    header.set_ndim (3);
+    header.ndim() = 3;
     b0 = new Image<value_type> (Image<value_type>::create (opt[0][0], header));
   }
 
   Image<value_type>* dkt = nullptr;
   opt = get_options ("dkt");
   if (opt.size()) {
-    header.set_ndim (4);
+    header.ndim() = 4;
     header.size(3) = 15;
     dkt = new Image<value_type> (Image<value_type>::create (opt[0][0], header));
   }

cmd/dwidenoise.cpp

@@ -224,7 +224,7 @@ void run ()
   Image<value_type> noise;
   opt = get_options("noise");
   if (opt.size()) {
-    header.set_ndim(3);
+    header.ndim() = 3;
     noise = Image<value_type>::create (opt[0][0], header);
   }
 

cmd/fixel2sh.cpp

@@ -66,7 +66,7 @@ void run ()
   H_out.datatype() = DataType::Float32;
   H_out.datatype().set_byte_order_native();
   const size_t sh_dim = H_in.ndim();
-  H_out.set_ndim (H_in.ndim() + 1);
+  H_out.ndim() = H_in.ndim() + 1;
   H_out.size (sh_dim) = N;
 
   auto sh = Image<float>::create (argument[1], H_out);

cmd/fixel2voxel.cpp

@@ -655,10 +655,10 @@ void run ()
   if (op == 10) { // count
     H_out.datatype() = DataType::UInt8;
   } else if (op == 13 || op == 14) { // dec
-    H_out.set_ndim (4);
+    H_out.ndim() = 4;
     H_out.size (3) = 3;
   } else if (op == 15 || op == 16 || op == 17) { // split_*
-    H_out.set_ndim (4);
+    H_out.ndim() = 4;
     uint32_t max_count = 0;
     for (auto l = Loop ("determining largest fixel count", in) (in); l; ++l)
       max_count = std::max (max_count, in.value().size());

cmd/fixelcfestats.cpp

@@ -196,7 +196,7 @@ void run() {
 
   // Create an image to store the fixel indices, if we had a fixel scratch buffer this would be cleaner
   Header index_header (input_header);
-  index_header.set_ndim(4);
+  index_header.ndim() = 4;
   index_header.size(3) = 2;
   auto fixel_index_image = Image<int32_t>::scratch (index_header);
   for (auto i = Loop ()(fixel_index_image);i; ++i)

cmd/fod2dec.cpp

@@ -261,7 +261,7 @@ void run () {
       auto fod_img = fod_hdr.get_image<value_type>().with_direct_io(3);
 
       auto dec_hdr = Header(fod_img);
-      dec_hdr.set_ndim(4);
+      dec_hdr.ndim() = 4;
       dec_hdr.size(3) = 3;
       Stride::set (dec_hdr, Stride::contiguous_along_axis (3, dec_hdr));
       dec_img = Image<value_type>::scratch(dec_hdr,"DEC map");
@@ -284,7 +284,7 @@ void run () {
 
     auto out_hdr = map_hdr.valid() ? Header(map_hdr) : Header(dec_img);
     out_hdr.datatype() = DataType::Float32;
-    out_hdr.set_ndim(4);
+    out_hdr.ndim() = 4;
     out_hdr.size(3) = 3;
     Stride::set (out_hdr, Stride::contiguous_along_axis (3, out_hdr));
     out_img = Image<value_type>::create(argument[1],out_hdr);

cmd/fod2fixel.cpp

@@ -109,7 +109,7 @@ class Segmented_FOD_receiver
     Segmented_FOD_receiver (const Header& header) :
         H (header)
     {
-      H.set_ndim (3);
+      H.ndim() = 3;
       H.datatype() = DataType::UInt64;
       H.datatype().set_byte_order_native();
       H.keyval()[Sparse::name_key] = str(typeid(FixelMetric).name());

cmd/label2colour.cpp

@@ -96,7 +96,7 @@ void run ()
     }
   }
 
-  H.set_ndim (4);
+  H.ndim() = 4;
   H.size (3) = 3;
   H.datatype() = DataType::UInt8;
   add_line (H.keyval()["comments"], "Coloured parcellation image generated by label2colour");

cmd/mraverageheader.cpp

@@ -89,7 +89,7 @@ void run ()
     auto H = compute_minimum_average_header (headers_in, resolution, padding, transform_header_with);
     H.datatype() = DataType::Bit;
     if (fill) {
-      H.set_ndim(dim);
+      H.ndim() = dim;
       if (dim == 4)
         H.size(3) = headers_in.back().size(3);
     }

cmd/mrcalc.cpp

@@ -583,8 +583,8 @@ void get_header (const StackEntry& entry, Header& header)
   }
 
   if (header.ndim() < entry.image->ndim()) 
-    header.set_ndim (entry.image->ndim());
-  for (size_t n = 0; n < std::min (header.ndim(), entry.image->ndim()); ++n) {
+    header.ndim() = entry.image->ndim();
+  for (size_t n = 0; n < std::min<size_t> (header.ndim(), entry.image->ndim()); ++n) {
     if (header.size(n) > 1 && entry.image->size(n) > 1 && header.size(n) != entry.image->size(n))
       throw Exception ("dimensions of input images do not match - aborting");
     header.size(n) = std::max (header.size(n), entry.image->size(n));

cmd/mrcat.cpp

@@ -84,7 +84,7 @@ void run () {
   if (axis >= ndims) ndims = axis+1;
 
   Header header_out (in[0]);
-  header_out.set_ndim (ndims);
+  header_out.ndim() = ndims;
 
   for (size_t i = 0; i < header_out.ndim(); i++) {
     if (header_out.size (i) <= 1) {
@@ -152,7 +152,7 @@ void run () {
       out.value() = in.value();
     };
 
-    ThreadedLoop ("concatenating \"" + image_in.name() + "\"...", image_in, 0, std::min (image_in.ndim(), image_out.ndim()))
+    ThreadedLoop ("concatenating \"" + image_in.name() + "\"...", image_in, 0, std::min<size_t> (image_in.ndim(), image_out.ndim()))
       .run (copy_func, image_in, image_out);
     if (axis < int(image_in.ndim()))
       axis_offset += image_in.size (axis);

cmd/mrconvert.cpp

@@ -114,7 +114,7 @@ void permute_DW_scheme (Header& H, const std::vector<int>& axes)
 template <class ImageType>
 inline std::vector<int> set_header (Header& header, const ImageType& input)
 {
-  header.set_ndim (input.ndim());
+  header.ndim() = input.ndim();
   for (size_t n = 0; n < header.ndim(); ++n) {
     header.size(n) = input.size(n);
     header.spacing(n) = input.spacing(n);
@@ -126,15 +126,15 @@ inline std::vector<int> set_header (Header& header, const ImageType& input)
   std::vector<int> axes;
   if (opt.size()) {
     axes = opt[0][0];
-    header.set_ndim (axes.size());
+    header.ndim() = axes.size();
     for (size_t i = 0; i < axes.size(); ++i) {
       if (axes[i] >= static_cast<int> (input.ndim()))
         throw Exception ("axis supplied to option -axes is out of bounds");
       header.size(i) = axes[i] < 0 ? 1 : input.size (axes[i]);
     }
     permute_DW_scheme (header, axes);
   } else {
-    header.set_ndim (input.ndim());
+    header.ndim() = input.ndim();
     axes.assign (input.ndim(), 0);
     for (size_t i = 0; i < axes.size(); ++i) {
       axes[i] = i;

cmd/mrmath.cpp

@@ -369,7 +369,7 @@ void run ()
 
     // Wipe any excess unary-dimensional axes
     while (header.size (header.ndim() - 1) == 1)
-      header.set_ndim (header.ndim() - 1);
+      header.ndim() = header.ndim() - 1;
 
     // Verify that dimensions of all input images adequately match
     for (size_t i = 1; i != num_inputs; ++i) {

cmd/mrmetric.cpp

@@ -413,7 +413,7 @@ void run ()
         output2mask = Header::scratch (midway_image_header, "-").get_image<bool>();
 
         Header new_header;
-        new_header.set_ndim(input1.ndim());
+        new_header.ndim() = input1.ndim();
         for (ssize_t dim=0; dim < 3; ++dim){
           new_header.size(dim) = midway_image_header.size(dim);
           new_header.spacing(dim) = midway_image_header.spacing(dim);

cmd/mrregister.cpp

@@ -787,7 +787,7 @@ void run ()
 
     if (warp1_filename.size()) {
       Header output_header (im2_image);
-      output_header.set_ndim(4);
+      output_header.ndim() = 4;
       output_header.size(3) =3;
       nl_registration.write_params_to_header (output_header);
       output_header.datatype() = DataType::from_command_line (DataType::Float32);
@@ -800,7 +800,7 @@ void run ()
 
     if (warp2_filename.size()) {
       Header output_header (im1_image);
-      output_header.set_ndim(4);
+      output_header.ndim() = 4;
       output_header.size(3) = 3;
       nl_registration.write_params_to_header (output_header);
       output_header.datatype() = DataType::from_command_line (DataType::Float32);
@@ -819,7 +819,7 @@ void run ()
 
     if (do_nonlinear) {
       Header deform_header (im1_transformed);
-      deform_header.set_ndim(4);
+      deform_header.ndim() = 4;
       deform_header.size(3) = 3;
       Image<default_type> deform_field = Image<default_type>::scratch (deform_header);
       Registration::Warp::compute_full_deformation (nl_registration.get_im2_to_mid_linear().inverse(),
@@ -859,7 +859,7 @@ void run ()
     if (do_nonlinear) {
       Header midway_header (*nl_registration.get_im1_to_mid());
       midway_header.datatype() = DataType::from_command_line (DataType::Float32);
-      midway_header.set_ndim (im1_image.ndim());
+      midway_header.ndim() = im1_image.ndim();
       if (midway_header.ndim() == 4)
         midway_header.size(3) = im1_image.size(3);
 

cmd/sh2power.cpp

@@ -58,7 +58,7 @@ void run () {
   if (spectrum)
     power_header.size (3) = 1 + lmax/2;
   else
-    power_header.set_ndim(3);
+    power_header.ndim() = 3;
   power_header.datatype() = DataType::Float32;
 
   auto power_data = Image<float>::create(argument[1], power_header);

cmd/shbasis.cpp

@@ -116,7 +116,7 @@ void check_and_update (Header& H, const conv_t conversion)
 
   // Need to mask out voxels where the DC term is zero
   Header header_mask (H);
-  header_mask.set_ndim (3);
+  header_mask.ndim() = 3;
   header_mask.datatype() = DataType::Bit;
   auto mask = Image<bool>::scratch (header_mask);
   size_t voxel_count = 0;

cmd/tckglobal.cpp

@@ -364,7 +364,7 @@ void run ()
   opt = get_options("eext");
   if (opt.size()) {
     INFO("Saving external energy to file");
-    header.set_ndim(3);
+    header.ndim() = 3;
     auto EextI = Image<float>::create (opt[0][0], header);
     threaded_copy(Eext->getEext(), EextI);
   }

cmd/tckmap.cpp

@@ -292,7 +292,7 @@ void run () {
   }
 
   if (header.ndim() > 3) {
-    header.set_ndim (3);
+    header.ndim() = 3;
     header.sanitise();
   }
 
@@ -328,7 +328,7 @@ void run () {
   opt = get_options ("dec");
   if (opt.size()) {
     writer_type = DEC;
-    header.set_ndim (4);
+    header.ndim() = 4;
     header.size (3) = 3;
     header.sanitise();
     Stride::set (header, Stride::contiguous_along_axis (3, header));
@@ -344,7 +344,7 @@ void run () {
       dirs.reset (new DWI::Directions::FastLookupSet (str(opt[0][0])));
     else
       dirs.reset (new DWI::Directions::FastLookupSet (to<size_t>(opt[0][0])));
-    header.set_ndim (4);
+    header.ndim() = 4;
     header.size(3) = dirs->size();
     header.sanitise();
     Stride::set (header, Stride::contiguous_along_axis (3, header));
@@ -367,7 +367,7 @@ void run () {
     const size_t lmax = opt[0][0];
     if (lmax % 2)
       throw Exception ("lmax for TODI must be an even number");
-    header.set_ndim (4);
+    header.ndim() = 4;
     header.size(3) = Math::SH::NforL (lmax);
     header.sanitise();
     Stride::set (header, Stride::contiguous_along_axis (3, header));