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/*
* Copyright (c) 2008-2018 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, you can obtain one at http://mozilla.org/MPL/2.0/
*
* MRtrix3 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
*
* For more details, see http://www.mrtrix.org/
*/
#include <set>
#include "command.h"
#include "image.h"
#include "image_helpers.h"
#include "transform.h"
#include "types.h"
#include "algo/copy.h"
using namespace MR;
using namespace App;
// TODO:
// * Operate on mask images rather than arbitrary images?
// * Remove capability to edit in-place - just deal with image swapping in the script?
// * Tests
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Directly edit the intensities within an image from the command-line";
DESCRIPTION
+ "A range of options are provided to enable direct editing of "
"voxel intensities based on voxel / real-space coordinates. "
"If only one image path is provided, the image will be edited in-place "
"(use at own risk); if input and output image paths are provided, the "
"output will contain the edited image, and the original image will not "
"be modified in any way.";
ARGUMENTS
+ Argument ("input", "the input image").type_image_in()
+ Argument ("output", "the (optional) output image").type_image_out().optional();
OPTIONS
+ Option ("plane", "fill one or more planes on a particular image axis").allow_multiple()
+ Argument ("axis").type_integer (0, 2)
+ Argument ("coord").type_sequence_int()
+ Argument ("value").type_float()
+ Option ("sphere", "draw a sphere with radius in mm").allow_multiple()
+ Argument ("position").type_sequence_float()
+ Argument ("radius").type_float()
+ Argument ("value").type_float()
+ Option ("voxel", "change the image value within a single voxel").allow_multiple()
+ Argument ("position").type_sequence_float()
+ Argument ("value").type_float()
+ Option ("scanner", "indicate that coordinates are specified in scanner space, rather than as voxel coordinates");
}
class Vox : public Eigen::Array3i
{ MEMALIGN (Vox)
public:
using Eigen::Array3i::Array3i;
Vox (const Eigen::Vector3& p) :
Eigen::Array3i { int(std::round (p[0])), int(std::round (p[1])), int(std::round (p[2])) } { }
bool operator< (const Vox& i) const {
return (i[0] == (*this)[0] ? (i[1] == (*this)[1] ? (i[2] < (*this)[2]) : (i[1] < (*this)[1])) : (i[0] < (*this)[0]));
}
};
const Vox voxel_offsets[6] = { { 0, 0, -1},
{ 0, 0, 1},
{ 0, -1, 0},
{ 0, 1, 0},
{-1, 0, 0},
{ 1, 0, 0} };
void run ()
{
bool inplace = (argument.size() == 1);
auto H = Header::open (argument[0]);
auto in = H.get_image<float> (inplace); // Need to set read/write flag
Image<float> out;
if (inplace) {
out = Image<float> (in);
} else {
if (std::string(argument[1]) == std::string(argument[0])) // Not ideal test - could be different paths to the same file
throw Exception ("Do not provide same image as input and output; instad specify image to be edited in-place");
out = Image<float>::create (argument[1], H);
copy (in, out);
}
Transform transform (H);
const bool scanner = get_options ("scanner").size();
if (scanner && H.ndim() < 3)
throw Exception ("Cannot specify scanner-space coordinates if image has less than 3 dimensions");
size_t operation_count = 0;
auto opt = get_options ("plane");
if (opt.size()) {
if (H.ndim() != 3)
throw Exception ("-plane option only works for 3D images");
if (scanner)
throw Exception ("-plane option cannot be used with scanner-space coordinates");
}
operation_count += opt.size();
for (auto p : opt) {
const size_t axis = p[0];
const auto coords = parse_ints (p[1]);
const float value = p[2];
const std::array<size_t, 2> loop_axes { { axis == 0 ? size_t(1) : size_t(0), axis == 2 ? size_t(1) : size_t(2) } };
for (auto c : coords) {
out.index (axis) = c;
for (auto outer = Loop(loop_axes[0]) (out); outer; ++outer) {
for (auto inner = Loop(loop_axes[1]) (out); inner; ++inner)
out.value() = value;
}
}
}
opt = get_options ("sphere");
if (opt.size() && H.ndim() != 3)
throw Exception ("-sphere option only works for 3D images");
operation_count += opt.size();
for (auto s : opt) {
const auto position = parse_floats (s[0]);
Eigen::Vector3 centre_scannerspace (position[0], position[1], position[2]);
const default_type radius = s[1];
const float value = s[2];
if (position.size() != 3)
throw Exception ("Centre of sphere must be defined using 3 comma-separated values");
Eigen::Vector3 centre_voxelspace (centre_scannerspace);
if (scanner)
centre_voxelspace = transform.scanner2voxel * centre_scannerspace;
else
centre_scannerspace = transform.voxel2scanner * centre_voxelspace;
std::set<Vox> processed;
vector<Vox> to_expand;
const Vox seed_voxel (centre_voxelspace);
processed.insert (seed_voxel);
to_expand.push_back (seed_voxel);
while (to_expand.size()) {
const Vox v (to_expand.back());
to_expand.pop_back();
const Eigen::Vector3 v_scanner = transform.voxel2scanner * v.matrix().cast<default_type>();
const default_type distance = (v_scanner - centre_scannerspace).norm();
if (distance < radius) {
if (!is_out_of_bounds (H, v)) {
assign_pos_of (v).to (out);
out.value() = value;
}
for (size_t i = 0; i != 6; ++i) {
const Vox v_adj (v + voxel_offsets[i]);
if (processed.find (v_adj) == processed.end()) {
processed.insert (v_adj);
to_expand.push_back (v_adj);
}
}
}
}
}
opt = get_options ("voxel");
operation_count += opt.size();
for (auto v : opt) {
const auto position = parse_floats (v[0]);
const float value = v[1];
if (position.size() != H.ndim())
throw Exception ("Image has " + str(H.ndim()) + " dimensions, but -voxel option position " + std::string(v[0]) + " provides only " + str(position.size()) + " coordinates");
if (scanner) {
Eigen::Vector3 p (position[0], position[1], position[2]);
p = transform.scanner2voxel * p;
const Vox voxel (p);
assign_pos_of (voxel).to (out);
for (size_t axis = 3; axis != out.ndim(); ++axis) {
if (std::round (position[axis]) != position[axis])
throw Exception ("Non-spatial coordinates provided using -voxel option must be provided as integers");
out.index(axis) = position[axis];
}
} else {
for (size_t axis = 0; axis != out.ndim(); ++axis) {
if (std::round (position[axis]) != position[axis])
throw Exception ("Voxel coordinates provided using -voxel option must be provided as integers");
out.index(axis) = position[axis];
}
}
out.value() = value;
}
if (!operation_count) {
if (inplace) {
WARN ("No edits specified; image will be unaffected");
} else {
WARN ("No edits specified; output image will be copy of input");
}
}
}
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