- modify mrd tools scripts of stream_recon and mrd_image_stream_to_png to support frequency dimension from MRD to ISMRMRD and vice versa.

- update MRD-ISMRMRD converters to take the image of 0th frequency dimension of MRD format to ISMRMRD to ignore frequency dimension, which has not equilvalence in ISMRMRD format.
- add cflags overwrite to avoid fortify_source error
- add version check for setuptools on meta.yaml to avoid setuptools.build_meta import failures.

Author: kekeke21

cpp/CMakeLists.txt

@@ -16,8 +16,13 @@ project(mrd VERSION ${MRD_VERSION_STRING})
 
 message(STATUS "MRD_VERSION_STRING: ${MRD_VERSION_STRING}")
 
-SET(CMAKE_CXX_FLAGS_DEBUG "-O0 -g")
-SET(CMAKE_C_FLAGS_DEBUG "-O0 -g")
+# if flags are already set, don't override them
+if (NOT DEFINED CMAKE_CXX_FLAGS_DEBUG)
+    SET(CMAKE_CXX_FLAGS_DEBUG "-O0 -g")
+endif ()
+if (NOT DEFINED CMAKE_C_FLAGS_DEBUG)
+    SET(CMAKE_C_FLAGS_DEBUG "-O0 -g")
+endif ()
 
 #Set the build type to Release if not specified
 if (NOT CMAKE_BUILD_TYPE)

cpp/mrd-tools/converters.cc

@@ -1054,8 +1054,8 @@ ISMRMRD::Image<T> convert(mrd::Image<T>& image) {
     for (int z = 0; z < im.getMatrixSizeZ(); z++) {
       for (int y = 0; y < im.getMatrixSizeY(); y++) {
         for (int x = 0; x < im.getMatrixSizeX(); x++) {
-          // ISMRMRD does not support frequency dimension from MRD image
-          // Take 0th image on frequency dimension from MRD to ISMRMRD
+          // MRD supports frequency as extra dimension, which does not exist in ISMRMRD format
+          // Take 0th image on frequency dimension from MRD to convert to ISMRMRD
           im(x, y, z, c) = image.data(c, z, y, x, 0);
         }
       }
@@ -2063,8 +2063,8 @@ mrd::Image<T> convert(ISMRMRD::Image<T>& im) {
     image.head.user_float.push_back(im.getUserFloat(i));
   }
 
-  // Add an extra singleton dimension from ISMRMRD to represent (channel, z, y, x, frequency) dimensions for MRD image
-  mrd::ImageData<T> data({im.getNumberOfChannels(), im.getMatrixSizeZ(), im.getMatrixSizeY(), im.getMatrixSizeX(), 0});
+  // Add an extra singleton dimension to represent (channel, z, y, x, frequency) dimensions for MRD image
+  mrd::ImageData<T> data({im.getNumberOfChannels(), im.getMatrixSizeZ(), im.getMatrixSizeY(), im.getMatrixSizeX(), 1});
   for (int c = 0; c < im.getNumberOfChannels(); c++) {
     for (int z = 0; z < im.getMatrixSizeZ(); z++) {
       for (int y = 0; y < im.getMatrixSizeY(); y++) {

cpp/mrd-tools/mrd_stream_recon.cc

@@ -187,7 +187,7 @@ int main(int argc, char** argv) {
           }
           slice = fftshift(slice);
 
-          std::array<size_t, 4> image_shape = {1, slice.shape(1), slice.shape(2), slice.shape(3)};
+          std::array<size_t, 5> image_shape = {1, slice.shape(1), slice.shape(2), slice.shape(3), 1}; // singleton frequency dimension added
           auto pixel_data = xt::sqrt(xt::abs(xt::sum(slice * xt::conj(slice), 0)));
 
           auto xoffset = (slice.shape(3) + 1) / 2 - (rNx + 1) / 2;
@@ -200,7 +200,7 @@ int main(int argc, char** argv) {
 
           mrd::Image<float> im;
           im.data = xt::zeros<float>(image_shape);
-          xt::view(im.data, 0, xt::all(), xt::all(), xt::all()) = combined;
+          xt::view(im.data, 0, xt::all(), xt::all(), xt::all(), 0) = combined;
 
           im.head.measurement_uid = acq.head.measurement_uid;
           im.head.field_of_view[0] = rFOVx;

cpp/mrd/types.h

@@ -985,7 +985,7 @@ struct Image {
     return yardl::shape(data, 3);
   }
 
-  yardl::Size Freqs() const {
+  yardl::Size Frequencies() const {
     return yardl::shape(data, 4);
   }
 

matlab/toolbox/+mrd/Image.m

@@ -48,7 +48,7 @@
       return
     end
 
-    function res = freqs(self)
+    function res = frequencies(self)
       res = size(self.data, ndims(self.data)-(4));
       return
     end

model/mrd_image.yml

@@ -98,7 +98,7 @@ Image<T>: !record
     slices: size(data, "z")
     rows: size(data, "y")
     cols: size(data, "x")
-    freqs: size(data, "frequency")
+    frequencies: size(data, "frequency")
 
 ImageUint16: Image<uint16>
 ImageInt16: Image<int16>

python/conda/meta.yaml

@@ -16,6 +16,7 @@ requirements:
   build:
     - python
     - pip
+    - setuptools >=65.5.0
   run:
     - python
     - ismrmrd-python >=1.14.2

python/mrd/tools/export_png_images.py

@@ -20,7 +20,7 @@ def export(input, output, verbose=False):
 
             for c in range(image.channels()):
                 for s in range(image.slices()):
-                    im = Image.fromarray(pixels[c, s, :, :], 'L')
+                    im = Image.fromarray(pixels[c, s, :, :, 0], 'L')    # 0th idx to ignore frequency dimension
                     filename = f"{output}{image_count:05d}.png"
                     im.save(filename, format='PNG')
                     if verbose:

python/mrd/tools/ismrmrd_to_mrd.py

@@ -514,7 +514,7 @@ def convert_image(ismrmrd_img: ismrmrd.Image) -> mrd.StreamItem:
             # If parsing fails, skip meta
             pass
 
-    data = ismrmrd_img.data
+    data = np.expand_dims(ismrmrd_img.data, axis=-1)    # add frequency dimension from ISMRMRD to MRD on the last axis
     dtype = data.dtype
     if dtype == np.uint16:
         img = mrd.Image[np.uint16](head=out_head, data=data.astype(np.uint16), meta=meta)

python/mrd/tools/mrd_to_ismrmrd.py

@@ -481,11 +481,12 @@ def convert_image(mrd_img) -> ismrmrd.Image:
     mrd_head = mrd_img.head
     data = mrd_img.data
 
-    # Get dimensions: data is (channels, z, y, x)
+    # Get dimensions: data is (channels, z, y, x, frequencies)
     channels = data.shape[0]
     z = data.shape[1]
     y = data.shape[2]
     x = data.shape[3]
+    frequencies = data.shape[4] # no equivalence in ISMRMRD
 
     # Build the ImageHeader first
     head = ismrmrd.ImageHeader()
@@ -585,7 +586,7 @@ def convert_image(mrd_img) -> ismrmrd.Image:
     # Note: resize signature is (nc, nz, ny, nx) - same order as MRD!
     img.resize(channels, z, y, x)
     img.setHead(head)
-    img.data[:] = data
+    img.data[:] = data[..., 0]    # Take 0th frequency dimension from mrd to ISMRMRD
 
     # Set attribute_string if present
     if attribute_string: