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Complex value support #47

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Complex value support #47

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66dc290
mrpeek: add support in backend for complex number display
jdtournier Dec 13, 2023
6e560bb
mrpeek: add commandline options and keyboard shortcuts to toggle comp…
jdtournier Dec 13, 2023
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72 changes: 56 additions & 16 deletions cmd/mrpeek.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,14 @@ using namespace VT;

vector<std::string> colourmap_choices_std;
vector<const char*> colourmap_choices_cstr;
const char* complex_choices [] = {
"real",
"imag",
"abs",
"arg",
"colour",
nullptr
};

enum ArrowMode { ARROW_SLICEVOL, ARROW_COLOUR, ARROW_CROSSHAIR, N_ARROW_MODES };

Expand All @@ -40,6 +48,7 @@ void usage ()
++entry;
} while (entry->name && !entry->special && !entry->is_colour);
colourmap_choices_cstr.reserve (colourmap_choices_std.size() + 1);

for (const auto& s : colourmap_choices_std)
colourmap_choices_cstr.push_back (s.c_str());
colourmap_choices_cstr.push_back (nullptr);
Expand Down Expand Up @@ -103,6 +112,11 @@ void usage ()
". Default is " + colourmap_choices_std[0] + ".")
+ Argument ("name").type_choice (colourmap_choices_cstr.data())

+ Option ("complex",
"for complex numbers, select which aspect to show. Choices are: " + join (complex_choices, ",") +
". Default is " + complex_choices[0] + ".")
+ Argument ("type").type_choice (complex_choices)

+ Option ("focus",
"set focus (crosshairs) at specified position, as a comma-separated "
"list of values. Use empty entries to leave as default (e.g. '-focus ,,100' "
Expand Down Expand Up @@ -130,7 +144,8 @@ void usage ()


using value_type = float;
using ImageType = Image<value_type>;
using cpx_value_type = cfloat;
using ImageType = Image<cpx_value_type>;
using Reslicer = Adapter::Reslice<Interp::Nearest, ImageType>;
using LinearReslicer = Adapter::Reslice<Interp::Linear, ImageType>;
using CubicReslicer = Adapter::Reslice<Interp::Cubic, ImageType>;
Expand All @@ -142,7 +157,8 @@ using CubicReslicer = Adapter::Reslice<Interp::Cubic, ImageType>;
// These will need to be moved into a struct/class eventually...
int levels = 32;
int x_axis, y_axis, slice_axis = 2, plot_axis = slice_axis, vol_axis = -1;
value_type pmin = DEFAULT_PMIN, pmax = DEFAULT_PMAX, zoom = 1.0;
int display_type = 0;
default_type pmin = DEFAULT_PMIN, pmax = DEFAULT_PMAX, zoom = 1.0;
bool crosshair = true, colorbar = true, orthoview = true, interactive = true;
bool do_plot = false, show_image = true, interpolate = false, show_text = true;
vector<int> focus (3, 0); // relative to original image grid
Expand All @@ -151,6 +167,18 @@ Sixel::ColourMaps colourmaps;
Sixel::ColourMaps plot_cmaps;



inline value_type get_scalar (const cpx_value_type val) {
switch (display_type) {
case 0: return std::real (val);
case 1: return std::imag (val);
case 2: return std::abs (val);
case 3: return std::arg (val);
case 4: return std::abs (val);
}
return 0.0;
}

inline std::string move_down (int n) {
if (interactive)
return move_cursor (Down, n);
Expand All @@ -164,7 +192,7 @@ inline std::string move_down (int n) {
// calculate percentile of a list of numbers
// implementation based on `mrthreshold` - can be merged with Math::median in due course
template <class Container>
value_type percentile (Container& data, default_type percentile)
default_type percentile (Container& data, default_type percentile)
{
// ignore nan
auto isnotfinite = [](typename Container::value_type val) { return !std::isfinite(val); };
Expand Down Expand Up @@ -236,7 +264,15 @@ inline std::string show_focus (ImageType& image)
}
out += "] ";

out += "| value: " + str(image.value());
out += "| value [";
switch (display_type) {
case 0: out += "real"; break;
case 1: out += "imag"; break;
case 2: out += "abs"; break;
case 3: out += "arg"; break;
case 4: out += "colour"; break;
}
out+= "]: " + str(image.value());

return out;
}
Expand All @@ -249,7 +285,7 @@ inline Reslicer get_regridder (ImageType& image, int with_slice_axis)
Header header_target (image);
default_type original_extent;
for (int d = 0; d < 3; ++d) {
const float new_voxel_size = (d == with_slice_axis) ? image.spacing(d) : 1.0f/zoom;
const default_type new_voxel_size = (d == with_slice_axis) ? image.spacing(d) : 1.0f/zoom;

original_extent = image.size(d) * image.spacing(d);

Expand All @@ -276,16 +312,16 @@ void autoscale (ImageType& image, Sixel::CMap& cmap)
const int y_dim = image_regrid.size(y_axis);
image_regrid.index(slice_axis) = focus[slice_axis];

vector<value_type> currentslice (x_dim*y_dim);
vector<default_type> currentslice (x_dim*y_dim);
size_t k = 0;
std::cerr.flush();
for (auto l = Loop (vector<size_t>({ size_t(x_axis), size_t(y_axis) }))(image_regrid); l; ++l) {
//std::cerr << "[" << image_regrid.index(0) << " " << image_regrid.index(1) << " " << image_regrid.index(2) << "] ";
currentslice[k++] = image_regrid.value();
currentslice[k++] = get_scalar (image_regrid.value());
}

value_type vmin = percentile(currentslice, pmin);
value_type vmax = percentile(currentslice, pmax);
default_type vmin = percentile(currentslice, pmin);
default_type vmax = percentile(currentslice, pmax);
cmap.set_scaling_min_max (vmin, vmax);
INFO("reset intensity range to " + str(vmin) + " - " +str(vmax));
}
Expand Down Expand Up @@ -333,7 +369,7 @@ void render_slice (InterpType& regrid, const Sixel::ViewPort& view, const Sixel:
regrid.index(y_axis) = y_dim-1-y;
for (int x = 0; x < x_dim; ++x) {
regrid.index(x_axis) = x_dim-1-x;
view(x,y) = cmap (regrid.value());
view(x,y) = cmap (get_scalar (regrid.value()));
}
}
}
Expand Down Expand Up @@ -381,16 +417,16 @@ std::string plot (ImageType& image, int plot_axis)
ssize_t current_index = image.index (plot_axis);
image.index(plot_axis) = 0;

std::vector<value_type> plotslice (image.size(plot_axis));
std::vector<value_type> plotslice_finite (image.size(plot_axis));
std::vector<default_type> plotslice (image.size(plot_axis));
std::vector<default_type> plotslice_finite (image.size(plot_axis));
size_t k = 0;
for (auto l = Loop (plot_axis)(image); l; ++l) {
plotslice[k] = image.value();
plotslice[k] = get_scalar (image.value());
plotslice_finite[k] = plotslice[k];
++k;
}
value_type vmin = percentile(plotslice_finite, 0); // non-finite values removed
value_type vmax = percentile(plotslice_finite, 100);
default_type vmin = percentile(plotslice_finite, 0); // non-finite values removed
default_type vmax = percentile(plotslice_finite, 100);
if (vmax == vmin) {
vmin -= 1e-3;
vmax += 1e-3;
Expand Down Expand Up @@ -654,6 +690,7 @@ void show_help ()
+ key ("f", "show / hide crosshairs")
+ key ("r", "reset focus")
+ key ("i", "toggle between nearest (default) and linear interpolation")
+ key ("z", "toggle between real, imag, abs & arg display for complex numbers")
+ key ("left mouse & drag", "move focus")
+ key ("right mouse & drag", "adjust brightness / contrast")
+ key ("Esc", "reset brightness / contrast")
Expand Down Expand Up @@ -834,6 +871,7 @@ class CallBack : public EventLoop::CallBack
case 'r': focus[x_axis] = std::round (image.size(x_axis)/2); focus[x_axis] = std::round (image.size(x_axis)/2);
focus[slice_axis] = std::round (image.size(slice_axis)/2); break;
case 'i': interpolate = !interpolate; break;
case 'z': display_type++; if (display_type>3) display_type = 0; break;
case '+': zoom *= 1.1; std::cout << ClearScreen; break;
case '-': zoom /= 1.1; std::cout << ClearScreen; break;
case ' ':
Expand Down Expand Up @@ -888,7 +926,7 @@ class CallBack : public EventLoop::CallBack

void run ()
{
auto image = Image<value_type>::open (argument[0]);
auto image = ImageType::open (argument[0]);

size_t projection_axes[3] = {get_options("sagittal").size(), get_options("coronal").size(), get_options("axial").size()};
size_t psum = 0;
Expand All @@ -904,6 +942,8 @@ void run ()

int colourmap_ID = get_option_value ("colourmap", 0);

display_type = get_option_value ("complex", 0);

do_plot = get_options ("plot").size();
plot_axis = get_option_value ("plot", plot_axis);
if (plot_axis >= int(image.ndim()))
Expand Down