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mrdegibbs: Warn on complex image input #3235

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mrdegibbs: Warn on complex image input #3235

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ec0b960
mrdegibbs: Warn on complex image input
Lestropie Nov 11, 2025
e3c7dfa
Merge branch 'master' into mrdegibbs_warning
Lestropie Nov 17, 2025
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20 changes: 11 additions & 9 deletions cmd/mrdegibbs.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -316,11 +316,9 @@ void run ()
if (minW >= maxW)
throw Exception ("minW must be smaller than maxW");

auto in = Image<value_type>::open (argument[0]);
Header header (in);

header.datatype() = DataType::from_command_line (DataType::Float32);
auto out = Image<value_type>::create (argument[1], header);
Header header_in(Header::open(argument[0]));
if (header_in.datatype().is_complex())
throw Exception("3.0.x version of mrdegibbs command is not compatible with complex-typed input image");

vector<size_t> slice_axes = { 0, 1 };
auto opt = get_options ("axes");
Expand All @@ -329,15 +327,15 @@ void run ()
vector<uint32_t> axes = parse_ints<uint32_t> (opt[0][0]);
if (axes.size() != 2)
throw Exception ("slice axes must be specified as a comma-separated 2-vector");
if (size_t(std::max (axes[0], axes[1])) >= header.ndim())
if (size_t(std::max (axes[0], axes[1])) >= header_in.ndim())
throw Exception ("slice axes must be within the dimensionality of the image");
if (axes[0] == axes[1])
throw Exception ("two independent slice axes must be specified");
slice_axes = { size_t(axes[0]), size_t(axes[1]) };
}

auto slice_encoding_it = header.keyval().find ("SliceEncodingDirection");
if (slice_encoding_it != header.keyval().end()) {
auto slice_encoding_it = header_in.keyval().find ("SliceEncodingDirection");
if (slice_encoding_it != header_in.keyval().end()) {
try {
const Metadata::BIDS::axis_vector_type slice_encoding_axis_onehot = Metadata::BIDS::axisid2vector (slice_encoding_it->second);
vector<size_t> auto_slice_axes = { 0, 0 };
Expand Down Expand Up @@ -369,7 +367,7 @@ void run ()
}

// build vector of outer axes:
vector<size_t> outer_axes (header.ndim());
vector<size_t> outer_axes (header_in.ndim());
std::iota (outer_axes.begin(), outer_axes.end(), 0);
for (const auto axis : slice_axes) {
auto it = std::find (outer_axes.begin(), outer_axes.end(), axis);
Expand All @@ -378,6 +376,10 @@ void run ()
outer_axes.erase (it);
}

auto in = header_in.get_image<value_type>();
Header header_out(header_in);
header_out.datatype() = DataType::from_command_line(DataType::Float32);
auto out = Image<value_type>::create(argument[1], header_out);
ThreadedLoop ("performing Gibbs ringing removal", in, outer_axes, slice_axes)
.run_outer (ComputeSlice (outer_axes, slice_axes, nshifts, minW, maxW, in, out));
}
Expand Down
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