File: 3dimagefilterstack.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 (183 lines) | stat: -rw-r--r-- 5,783 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
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
/* -*- 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 <iostream>
#include <iomanip>
#include <string>
#include <sstream>
#include <stdexcept>

#include <mia/3d/filter.hh>
#include <mia/3d/imageio.hh>
#include <mia/core.hh>

using namespace std;
using namespace mia;

size_t log10(size_t x)
{
	int result = 0;
	while (x > 0) {
		++result;
		x /= 10;
	}
	return result;
}

const SProgramDescription g_description = {
	{pdi_group, "Analysis, filtering, combining, and segmentation of 3D images"}, 

	{pdi_short, "Filter a series of 3D images."}, 

	{pdi_description, "This program is used to filter and convert a consecutive numbered series "
	 "gray of scale images. File names must follow the pattern 'dataXXXX.v' "
	 "(X being digits), i.e. the numbering comes right before the dot. "}, 

	{pdi_example_descr, "Run a mean-least-varaiance filter on a series of images that follow the " 
	 "numbering pattern imageXXXX.hdr and store the output in images filteredXXXX.hdr"}, 

	{pdi_example_code, "-i image0000.hdr -o filtered -t hdr mlv:w=2"}
}; 


int do_main( int argc, char *argv[] )
{

	string in_filename;
	string out_filename;
	string out_type;

	const auto& filter_plugins = C3DFilterPluginHandler::instance();
	const auto& imageio = C3DImageIOPluginHandler::instance();


	CCmdOptionList options(g_description);
	options.add(make_opt( in_filename, "in-file", 'i', "input image(s) to be filtered", CCmdOptionFlags::required_input, &imageio));
	options.add(make_opt( out_filename, "out-file", 'o', "output file name base, numbers are added accorfing to the input "
			      "file pattern, and the file  extension is added according to the 'type' option.", 
			      CCmdOptionFlags::required, &imageio));
	options.add(make_opt( out_type, imageio.get_set(), "type", 't',"output file type", CCmdOptionFlags::required));
	
	options.add(make_help_opt( "help-plugins", 0,
				   "give some help about the filter plugins", 
				   new TPluginHandlerHelpCallback<C3DFilterPluginHandler>)); 

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


	auto filter_chain = options.get_remaining();

	cvdebug() << "IO supported types: " << imageio.get_plugin_names() << "\n";
	cvdebug() << "supported filters: " << filter_plugins.get_plugin_names() << "\n";

	if ( filter_chain.empty() )
		cvwarn() << "no filters given, just copy\n";

	if ( in_filename.empty() )
		throw runtime_error("'--in-file' ('i') option required");

	if ( out_filename.empty() )
		throw runtime_error("'--out-base' ('o') option required");

	bool use_src_format = out_type.empty();
		
	string out_suffix = imageio.get_preferred_suffix(out_type); 


	//	CHistory::instance().append(argv[0], revision, options);

	list<P3DFilter> filters;

	for (auto i = filter_chain.begin();  i != filter_chain.end(); ++i) {
		cvdebug() << "Prepare filter " << *i << endl;
		auto filter = filter_plugins.produce(*i);
		if (!filter){
			stringstream error;
			error << "Filter " << *i << " not found";
			throw invalid_argument(error.str());
		}
		filters.push_back(filter);
	}

	size_t start_filenum = 0;
	size_t end_filenum  = 0;
	size_t format_width = 0;

	string src_basename = get_filename_pattern_and_range(in_filename, start_filenum, end_filenum, format_width);
	if (start_filenum >= end_filenum)
		throw invalid_argument(string("no files match pattern ") + src_basename);

	char new_line = cverb.show_debug() ? '\n' : '\r';
#ifndef WIN32
	time_t start_time = time(NULL);
#endif
	for (size_t i = start_filenum; i < end_filenum; ++i) {

		string src_name = create_filename(src_basename.c_str(), i);
		cvmsg() << new_line << "Filter: " << i <<" out of "<< "[" << start_filenum<< "," << end_filenum << "]" ;
		auto in_image_list = imageio.load(src_name);
		if (in_image_list.get() && in_image_list->size()) {

			if (use_src_format)
				out_type = in_image_list->get_source_format();

			auto filter_name = filter_chain.begin();

			for (auto f = filters.begin(); f != filters.end(); ++f, ++filter_name) {
				cvdebug() << "Run filter: " << *filter_name << "\n";
				for (auto i = in_image_list->begin();
				     i != in_image_list->end(); ++i) {
					*i = (*f)->filter(**i);
				}
			}

			stringstream ss;
			ss << out_filename << setw(format_width) << setfill('0') << i << "." << out_suffix;
			cvdebug() << "Save to " << ss.str() << ", format = " << out_type << "\n";

			if ( !imageio.save(ss.str(), *in_image_list) ){
				string not_save = ("unable to save result to ") + ss.str();
				throw runtime_error(not_save);

			}
		}
#ifndef WIN32
		if (cverb.shows(vstream::ml_message)) {
			char esttime[30];
			time_t est_end = (( end_filenum - start_filenum) * (time(NULL) - start_time)) /
				(i - start_filenum + 1) + start_time;
			ctime_r(&est_end, esttime);
			char *est = esttime;
			while (*est != '\n' && *est != 0)
				++est;
			if (*est == '\n')
				*est = ' ';
			cvmsg() << ", estimated finish at: " <<  esttime;
		}
#endif
	}
	cvmsg() << "\n";
	return EXIT_SUCCESS;

}

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