File: 3dnrreg.cc

package info (click to toggle)
mia 2.2.2-1
  • links: PTS, VCS
  • area: main
  • in suites: jessie, jessie-kfreebsd
  • size: 13,532 kB
  • ctags: 16,800
  • sloc: cpp: 137,909; python: 1,057; ansic: 998; sh: 146; xml: 127; csh: 24; makefile: 13
file content (138 lines) | stat: -rw-r--r-- 4,873 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
/* -*- mia-c++  -*-
 *
 * This file is part of MIA - a toolbox for medical image analysis 
 * Copyright (c) Leipzig, Madrid 1999-2014 Gert Wollny
 *
 * MIA is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program 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.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with MIA; if not, see <http://www.gnu.org/licenses/>.
 *
 */

#include <boost/algorithm/minmax_element.hpp>
#include <sstream>
#include <iomanip>

#include <mia/core.hh>

#include <mia/3d.hh>

NS_MIA_USE
using namespace boost;
using namespace std;

const SProgramDescription g_description = {
	{pdi_group, "Work in progress"},
	
	{pdi_short, "Non-linear registration of 3D images."}, 

	{pdi_description, "This program implements 3D gray scale image registration but "
	 "is currently not funcioning"}
}; 


// set op the command line parameters and run the registration
int do_main(int argc, char **argv)
{
	CCmdOptionList options(g_description);

	string src_filename;
	string out_filename;
	string def_filename;
	string ref_filename;
	string cost_function("ssd");
	string regmodel("navier");
	string timestep("fluid");
	int start_size = 16;
	PSplineKernel interpolator_kernel;
	int max_iter = 200;
	float epsilon = 0.01;
	bool save_steps = false;

	const C3DImageCostPluginHandler::Instance&  icph = C3DImageCostPluginHandler::instance();

	options.add(make_opt( src_filename, "in-file", 'i', "input image (floating image)", CCmdOptionFlags::required_input));
	options.add(make_opt( ref_filename, "ref-file", 'r', "reference image", CCmdOptionFlags::required_input));
	options.add(make_opt( out_filename, "out-file", 'o', "output vector field", CCmdOptionFlags::required_output));
	options.add(make_opt( def_filename, "def-file", 'd', "deformed output image", CCmdOptionFlags::output));
	options.add(make_opt( regmodel, "regmodel", 'm', "registration model"));
	options.add(make_opt( timestep, "timestep", 't', "time setp"));
	options.add(make_opt( start_size, "mgsize", 's', "multigrid start size"));
	options.add(make_opt( max_iter, "max-iter", 'n', ",maximum number of iterations"));
	options.add(make_opt( cost_function, "cost", 'c', "cost function"));
	options.add(make_opt( interpolator_kernel, "bspline:d=3", "interpolator", 'p', "image interpolator kernel"));
	options.add(make_opt( epsilon, "epsilon", 'e', "relative accuracy to stop registration"
				    " at a multi-grid level"));
	options.add(make_opt( save_steps, "save-steps", 0, "save the steps of the registration in images"));

	if (options.parse(argc, argv) != CCmdOptionList::hr_no)
		return EXIT_SUCCESS; 

	P3DImageCost cost = icph.produce(cost_function.c_str());
	P3DRegModel model = C3DRegModelPluginHandler::instance().produce(regmodel.c_str());
	P3DRegTimeStep time_step = C3DRegTimeStepPluginHandler::instance().produce(timestep.c_str());


	if (src_filename.empty() || ref_filename.empty() || out_filename.empty()) {
		cerr << "input, reference and output file names are required\n";
		return EXIT_FAILURE;
	}

	if (!cost || !model || !time_step)
		return EXIT_FAILURE;


	const C3DImageIOPluginHandler::Instance&  imageio = C3DImageIOPluginHandler::instance();
	typedef C3DImageIOPluginHandler::Instance::PData PImageVector;


	PImageVector reference = imageio.load(ref_filename);
	PImageVector source    = imageio.load(src_filename);

	if (!reference || reference->size() < 1) {
		cerr << "no image found in " << ref_filename << "\n";
		return EXIT_FAILURE;
	}

	if (!source || source->size() < 1) {
		cerr << "no image found in " << src_filename << "\n";
		return EXIT_FAILURE;
	}

	C3DInterpolatorFactory ipfactory(interpolator_kernel, "mirror");

	C3DImageRegister reg(start_size, *cost, max_iter, *model, *time_step, ipfactory, epsilon, save_steps);

	P3DFVectorfield regfield = reg(**source->begin(), **reference->begin());
	C3DIOVectorfield outfield(regfield->get_size());
	copy(regfield->begin(), regfield->end(), outfield.begin());

	if (!C3DVFIOPluginHandler::instance().save(out_filename, outfield)){
		cerr << "Unable to save result vector field to " << out_filename << "\n";
		return EXIT_FAILURE;
	}

	if (!def_filename.empty()) {
		C3DImageVector vimg;
		vimg.push_back(filter(FDeformer3D(*regfield, ipfactory), **source->begin()));
		if (!imageio.save(def_filename, vimg)) {
			cerr << "Unable to save result image to " << def_filename << "\n";
			return EXIT_FAILURE;
		}

	}
	return EXIT_SUCCESS;
}


#include <mia/internal/main.hh>
MIA_MAIN(do_main)