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Merge pull request #40 from MRtrix3/notext
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mrpeek: added no text mode, modified boolean cmd line options
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@jdtournier
jdtournier authored Nov 17, 2020
2 parents 99892e5 + c3fddd2 commit 5b6b335
Showing 1 changed file with 83 additions and 60 deletions.
143 changes: 83 additions & 60 deletions cmd/mrpeek.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -67,22 +67,17 @@ void usage ()

OPTIONS
#ifndef MRTRIX_WINDOWS
+ Option ("interactive",
"interactive mode. Default is true.")
+ Argument ("yesno").type_bool()
+ Option ("batch",
"disables interactive mode")
#endif
+ Option ("axis",
"specify projection of slice, as an integer representing the slice normal: "
"0: L/R (sagittal); 1: A/P (coronal); 2 I/S (axial). Default is 2 (axial). ")
+ Argument ("index").type_integer (0)
+ Option ("sagittal",
"view sagittal projection only. Default: orthoview")

+ Option ("slice",
"select slice to display")
+ Argument ("number").type_integer(0)
+ Option ("coronal",
"view coronal projection only. Default: orthoview")

+ Option ("orthoview",
"display three orthogonal or a single plane. Default is true.")
+ Argument ("yesno").type_bool()
+ Option ("axial",
"view axial projection only. Default: orthoview")

+ Option ("plot",
"specify plot dimension: "
Expand All @@ -108,18 +103,29 @@ void usage ()
". Default is " + colourmap_choices_std[0] + ".")
+ Argument ("name").type_choice (colourmap_choices_cstr.data())

+ Option ("crosshairs",
"draw crosshairs at specified position. Set to negative position to hide.")
+ Argument ("x").type_integer()
+ Argument ("y").type_integer()
+ 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' "
"to place the focus on slice 100 along the z-axis, or '-focus ,,,4' to "
"select volume 4).")
+ Argument ("pos").type_sequence_float()

+ Option ("levels",
"number of intensity levels in the colourmap. Default is 32.")
+ Argument ("number").type_integer (2)

+ Option ("zoom",
"scale the image size by the supplied factor")
+ Argument ("factor").type_float();
+ Argument ("factor").type_float()

+ Option ("notext",
"omit text output to show only the sixel image")

+ Option ("nocrosshairs",
"do not render crosshairs at the focus")

+ Option ("noimage",
"do not render the main image");
}


Expand All @@ -138,7 +144,7 @@ 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;
bool crosshair = true, colorbar = true, orthoview = true, interactive = true;
bool do_plot = false, show_image = true, interpolate = false;
bool do_plot = false, show_image = true, interpolate = false, show_text = true;
vector<int> focus (3, 0); // relative to original image grid
ArrowMode x_arrow_mode = ARROW_SLICEVOL, arrow_mode = x_arrow_mode;
Sixel::ColourMaps colourmaps;
Expand Down Expand Up @@ -426,7 +432,7 @@ std::string plot (ImageType& image, int plot_axis)
assert(y < y_dim);
assert(y >= 0);

if ((plot_axis < 3 && index == focus[plot_axis]) || (plot_axis > 2 && index == current_index)) {
if (crosshair && ((plot_axis < 3 && index == focus[plot_axis]) || (plot_axis > 2 && index == current_index))) {
// focus position: draw line
for (int r = 0; r < y_offset; ++r)
canvas (x_offset+x, r) = CROSSHAIR_COLOUR;
Expand Down Expand Up @@ -461,9 +467,9 @@ std::string plot (ImageType& image, int plot_axis)

// encode buffer and print out:
std::string out = move_down (2);
out += CarriageReturn + str(vmax) + move_down(1) + CarriageReturn
+ encoder.write()
+ ClearLine + str(vmin)
if (show_text) out += CarriageReturn + str(vmax) + move_down(1) + CarriageReturn;
out += encoder.write();
if (show_text) out += ClearLine + str(vmin)
+ move_down(1) + CarriageReturn + ClearLine
+ "plot axis: " + str(plot_axis) + " | x range: [ 0 " + str(plotslice.size() - 1) + " ]";

Expand Down Expand Up @@ -494,7 +500,7 @@ std::string display_image (ImageType& image, const Sixel::CMap& cmap, int colour
Sixel::Encoder encoder (colourbar_offset + regrid[0].size(1)+regrid[1].size(0)+regrid[2].size(0),
panel_y_dim, colourmaps);

draw_colourbar (encoder.viewport (0, 0, COLOURBAR_WIDTH), cmap);
if (colorbar) draw_colourbar (encoder.viewport (0, 0, COLOURBAR_WIDTH), cmap);


int x_pos = colourbar_offset;
Expand Down Expand Up @@ -532,7 +538,7 @@ std::string display_image (ImageType& image, const Sixel::CMap& cmap, int colour
const int y_dim = regrid.size (y_axis);

Sixel::Encoder encoder (colourbar_offset+x_dim, y_dim, colourmaps);
draw_colourbar (encoder.viewport (0, 0, COLOURBAR_WIDTH), cmap);
if (colorbar) draw_colourbar (encoder.viewport (0, 0, COLOURBAR_WIDTH), cmap);

auto view = encoder.viewport(colourbar_offset, 0);
display_slice (image, regrid, view, cmap);
Expand Down Expand Up @@ -574,23 +580,26 @@ std::string display (ImageType& image, Sixel::ColourMaps& colourmaps)

if (!cmap.scaling_set())
autoscale (image, cmap);

out += ClearLine;
if (arrow_mode == ARROW_COLOUR)
out += TextForegroundYellow;
out += str(cmap.max(),4) + TextReset + move_down(1) + position_cursor_at_col (2);
if (show_text) {
out += ClearLine;
if (arrow_mode == ARROW_COLOUR)
out += TextForegroundYellow;
out += str(cmap.max(),4) + TextReset + move_down(1) + position_cursor_at_col (2);
}

out += display_image (image, cmap, 2*COLOURBAR_WIDTH) + CarriageReturn + ClearLine;

if (arrow_mode == ARROW_COLOUR)
out += TextForegroundYellow;
out += str(cmap.min(), 4) + TextReset + move_down(1) + CarriageReturn;
if (show_text) {
if (arrow_mode == ARROW_COLOUR)
out += TextForegroundYellow;
out += str(cmap.min(), 4) + TextReset + move_down(1) + CarriageReturn;
}
}


out += show_focus(image);
if (show_text) out += show_focus(image);

if (orthoview) {
if (interactive && orthoview && show_text) {
out += " | active: ";
switch (slice_axis) {
case (0): out += std::string (TextUnderscore) + "s" + TextReset + "agittal"; break;
Expand All @@ -600,7 +609,7 @@ std::string display (ImageType& image, Sixel::ColourMaps& colourmaps)
};
}

if (interactive)
if (interactive && show_text)
out += std::string(" | help: ") + TextUnderscore + "?" + TextReset;
if (do_plot)
out += plot (image, plot_axis);
Expand Down Expand Up @@ -637,6 +646,7 @@ void show_help ()
+ key ("a / s / c", "axial / sagittal / coronal projection")
+ key ("o", "toggle orthoview")
+ key ("m", "toggle image display")
+ key ("t", "toggle text overlay")
+ key ("v", "choose volume dimension")
+ key ("- / +", "zoom out / in")
+ key ("x / <space>", "toggle arrow key crosshairs control")
Expand Down Expand Up @@ -735,7 +745,6 @@ class CallBack : public EventLoop::CallBack
if (need_update) {
need_update = false;
std::cout << CursorHome << display (image, colourmaps);
//std::cout << "UPDATE ";
std::cout.flush();
}
return true;;
Expand Down Expand Up @@ -820,6 +829,7 @@ class CallBack : public EventLoop::CallBack
case 's': slice_axis = 0; if (!orthoview) std::cout << ClearScreen; break;
case 'c': slice_axis = 1; if (!orthoview) std::cout << ClearScreen; break;
case 'o': orthoview = !orthoview; std::cout << ClearScreen; break;
case 't': show_text = colorbar = !show_text; std::cout << ClearScreen; break;
case 'm': show_image = !show_image; std::cout << ClearScreen; break;
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;
Expand Down Expand Up @@ -880,15 +890,17 @@ void run ()
{
auto image = Image<value_type>::open (argument[0]);

slice_axis = get_option_value ("axis", slice_axis);
size_t projection_axes[3] = {get_options("sagittal").size(), get_options("coronal").size(), get_options("axial").size()};
size_t psum = 0;
for (int i = 0; i < 3; ++i) {
if (projection_axes[i]) { ++psum; slice_axis = i; }
if (psum > 1) throw Exception("Projection axes options are mutually exclusive.");
}
orthoview = psum == 0;
vol_axis = image.ndim() > 3 ? 3 : -1;
focus[slice_axis] = get_option_value ("slice", image.size(slice_axis)/2);
set_axes();
focus[x_axis] = std::round (image.size(x_axis)/2);
focus[y_axis] = std::round (image.size(y_axis)/2);

if (focus[slice_axis] >= image.size(slice_axis))
throw Exception("slice " + str(focus[slice_axis]) + " exceeds image size (" + str(image.size(slice_axis)) + ") in axis " + str(slice_axis));
for (int a = 0; a < 3; ++a)
focus[a] = std::round (image.size(a)/2.0);

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

Expand Down Expand Up @@ -916,20 +928,26 @@ void run ()
pmax = opt[0][1];
}

opt = get_options ("crosshairs");
opt = get_options ("focus");
if (opt.size()) {
int x = opt[0][0];
int y = opt[0][1];
if (x<0 || y<0) {
crosshair = false;
} else {
focus[x_axis] = opt[0][0];
focus[y_axis] = opt[0][1];
vector<default_type> p = opt[0][0];
if (p.size() > image.ndim())
throw Exception ("number of indices passed to -focus option exceeds image dimensions");
for (unsigned int n = 0; n < p.size(); ++n) {
if (std::isfinite (p[n])) {
p[n] = Math::round<default_type>(p[n]);
if (p[n] < 0 || p[n] > image.size(n)-1)
throw Exception ("position passed to -focus option is out of bounds for axis "+str(n));
if (n < 3)
focus[n] = p[n];
else
image.index(n) = p[n];
}
}
}

//CONF option: MRPeekOrthoView
orthoview = get_option_value ("orthoview", File::Config::get_bool ("MRPeekOrthoView", orthoview));
if (get_options ("nocrosshairs").size())
crosshair = false;

//CONF option: MRPeekScaleImage
zoom = get_option_value ("zoom", MR::File::Config::get_float ("MRPeekZoom", zoom));
Expand All @@ -938,17 +956,22 @@ void run ()
INFO("zoom: " + str(zoom));
zoom /= std::min (std::min (image.spacing(0), image.spacing(1)), image.spacing(2));

#ifndef MRTRIX_WINDOWS
//CONF option: MRPeekInteractive
if (!interactive or !get_option_value ("interactive", File::Config::get_bool ("MRPeekInteractive", true))) {
#endif
colorbar = show_text = !get_options ("notext").size();
show_image = !get_options ("noimage").size();

#ifdef MRTRIX_WINDOWS
interactive = false;
std::cout << display (image, colourmaps) << "\n";
#else
interactive = isatty (STDOUT_FILENO);
if (get_options ("batch").size())
interactive = false;

if (!interactive) {
std::cout << display (image, colourmaps) << "\n";
return;
#ifndef MRTRIX_WINDOWS
}


try {
// start loop
enter_raw_mode();
Expand Down

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