Mercurial > hg > orthanc-wsi

annotate Applications/DicomToTiff.cpp @ 217:20bc074ec19a

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Viewer can display DICOM pyramids whose tile sizes vary across levels
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 12 Jan 2021 14:24:18 +0100
parents 1e864138f0da
children 49f647ed1b4c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1 /**
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
2 * Orthanc - A Lightweight, RESTful DICOM Store
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
4 * Department, University Hospital of Liege, Belgium
214
1e864138f0da upgrade to year 2021
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 199
diff changeset
5 * Copyright (C) 2017-2021 Osimis S.A., Belgium
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
6 *
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
7 * This program is free software: you can redistribute it and/or
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
8 * modify it under the terms of the GNU Affero General Public License
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
9 * as published by the Free Software Foundation, either version 3 of
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
10 * the License, or (at your option) any later version.
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
11 *
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
12 * This program is distributed in the hope that it will be useful, but
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
13 * WITHOUT ANY WARRANTY; without even the implied warranty of
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
15 * Affero General Public License for more details.
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
16 *
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
17 * You should have received a copy of the GNU Affero General Public License
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
19 **/
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
20
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
21
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
22 #include "../Framework/DicomToolbox.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
23 #include "../Framework/ImageToolbox.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
24 #include "../Framework/Inputs/DicomPyramid.h"
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
25 #include "../Framework/Inputs/TiledPyramidStatistics.h"
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
26 #include "../Framework/Outputs/HierarchicalTiffWriter.h"
196
b0bd22077cd8 sharing code with orthanc-stone
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 194
diff changeset
27 #include "../Resources/Orthanc/Stone/OrthancHttpConnection.h"
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
28
199
a1c265cb2174 replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 196
diff changeset
29 #include <Compatibility.h> // For std::unique_ptr
192
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 175
diff changeset
30 #include <Logging.h>
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 175
diff changeset
31 #include <OrthancException.h>
59
7a3853d51c45 Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
32
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
33 #include "ApplicationToolbox.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
34
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
35
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
36 static const char* OPTION_COLOR = "color";
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
37 static const char* OPTION_HELP = "help";
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
38 static const char* OPTION_INPUT = "input";
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
39 static const char* OPTION_JPEG_QUALITY = "jpeg-quality";
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
40 static const char* OPTION_OUTPUT = "output";
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
41 static const char* OPTION_REENCODE = "reencode";
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
42 static const char* OPTION_VERBOSE = "verbose";
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
43 static const char* OPTION_VERSION = "version";
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
44
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
45 static bool ParseParameters(int& exitStatus,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
46 boost::program_options::variables_map& options,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
47 int argc,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
48 char* argv[])
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
49 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
50 // Declare the supported parameters
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
51 boost::program_options::options_description generic("Generic options");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
52 generic.add_options()
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
53 (OPTION_HELP, "Display this help and exit")
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
54 (OPTION_VERSION, "Output version information and exit")
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
55 (OPTION_VERBOSE, "Be verbose in logs")
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
56 ;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
57
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
58 boost::program_options::options_description source("Options for the source DICOM image");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
59 source.add_options()
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
60 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
61 "URL to the REST API of the target Orthanc server")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
62 ;
125
7a3f4d580625 SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 115
diff changeset
63 OrthancWSI::ApplicationToolbox::AddRestApiOptions(source);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
64
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
65 boost::program_options::options_description target("Options for the target TIFF image");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
66 target.add_options()
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
67 (OPTION_COLOR, boost::program_options::value<std::string>(),
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
68 "Color of the background for missing tiles (e.g. \"255,0,0\")")
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
69 (OPTION_REENCODE, boost::program_options::value<bool>(),
31
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 8
diff changeset
70 "Whether to re-encode each tile in JPEG (no transcoding, much slower) (Boolean)")
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
71 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(),
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
72 "Set quality level for JPEG (0..100)")
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
73 ;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
74
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
75 boost::program_options::options_description hidden;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
76 hidden.add_options()
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
77 (OPTION_INPUT, boost::program_options::value<std::string>(),
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
78 "Orthanc identifier of the input series of interest")
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
79 (OPTION_OUTPUT, boost::program_options::value<std::string>(),
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
80 "Output TIFF file");
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
81
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
82 boost::program_options::options_description allWithoutHidden;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
83 allWithoutHidden.add(generic).add(source).add(target);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
84
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
85 boost::program_options::options_description all = allWithoutHidden;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
86 all.add(hidden);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
87
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
88 boost::program_options::positional_options_description positional;
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
89 positional.add(OPTION_INPUT, 1);
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
90 positional.add(OPTION_OUTPUT, 1);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
91
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
92 bool error = false;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
93
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
94 try
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
95 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
96 boost::program_options::store(boost::program_options::command_line_parser(argc, argv).
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
97 options(all).positional(positional).run(), options);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
98 boost::program_options::notify(options);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
99 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
100 catch (boost::program_options::error& e)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
101 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
102 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
103 error = true;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
104 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
105
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
106 if (!error &&
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
107 options.count(OPTION_HELP) == 0 &&
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
108 options.count(OPTION_VERSION) == 0)
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
109 {
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
110 if (options.count(OPTION_INPUT) != 1)
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
111 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
112 LOG(ERROR) << "No input series was specified";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
113 error = true;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
114 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
115
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
116 if (options.count(OPTION_OUTPUT) != 1)
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
117 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
118 LOG(ERROR) << "No output file was specified";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
119 error = true;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
120 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
121 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
122
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
123 if (error || options.count(OPTION_HELP))
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
124 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
125 std::cout << std::endl
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
126 << "Usage: " << argv[0] << " [OPTION]... [INPUT] [OUTPUT]"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
127 << std::endl
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
128 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research."
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
129 << std::endl << std::endl
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
130 << "Convert a DICOM image for digital pathology stored in some Orthanc server as a" << std::endl
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
131 << "standard hierarchical TIFF (whose tiles are all encoded using JPEG)."
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
132 << std::endl;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
133
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
134 std::cout << allWithoutHidden << "\n";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
135
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
136 if (error)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
137 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
138 exitStatus = -1;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
139 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
140
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
141 return false;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
142 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
143
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
144 if (options.count(OPTION_VERSION))
8
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
145 {
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
146 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]);
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
147 return false;
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
148 }
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
149
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
150 if (options.count(OPTION_VERBOSE))
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
151 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
152 Orthanc::Logging::EnableInfoLevel(true);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
153 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
154
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
155 return true;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
156 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
157
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
158
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
159
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
160 static Orthanc::ImageAccessor* CreateEmptyTile(const OrthancWSI::IPyramidWriter& writer,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
161 const boost::program_options::variables_map& options)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
162 {
199
a1c265cb2174 replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 196
diff changeset
163 std::unique_ptr<Orthanc::ImageAccessor> tile
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
164 (OrthancWSI::ImageToolbox::Allocate(writer.GetPixelFormat(),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
165 writer.GetTileWidth(),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
166 writer.GetTileHeight()));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
167
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
168 uint8_t red = 255;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
169 uint8_t green = 255;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
170 uint8_t blue = 255;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
171
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
172 if (options.count(OPTION_COLOR))
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
173 {
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
174 OrthancWSI::ApplicationToolbox::ParseColor(red, green, blue, options[OPTION_COLOR].as<std::string>());
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
175 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
176
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
177 OrthancWSI::ImageToolbox::Set(*tile, red, green, blue);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
178
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
179 return tile.release();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
180 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
181
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
182
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
183
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
184 static void Run(OrthancWSI::ITiledPyramid& source,
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
185 const boost::program_options::variables_map& options)
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
186 {
167
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
187 bool reencode = (options.count(OPTION_REENCODE) &&
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
188 options[OPTION_REENCODE].as<bool>());
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
189
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
190 Orthanc::PhotometricInterpretation targetPhotometric;
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
191
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
192 if (reencode)
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
193 {
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
194 // The DicomToTiff tool only creates TIFF images with JPEG tiles (*)
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
195 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422;
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
196 }
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
197 else
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
198 {
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
199 targetPhotometric = source.GetPhotometricInterpretation();
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
200 }
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
201
217
20bc074ec19a Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 214
diff changeset
202 OrthancWSI::ImageToolbox::CheckConstantTileSize(source); // (**)
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
203 OrthancWSI::HierarchicalTiffWriter target(options[OPTION_OUTPUT].as<std::string>(),
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
204 source.GetPixelFormat(),
167
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
205 OrthancWSI::ImageCompression_Jpeg, // (*)
217
20bc074ec19a Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 214
diff changeset
206 source.GetTileWidth(0), // (**)
20bc074ec19a Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 214
diff changeset
207 source.GetTileHeight(0), // (**)
167
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
208 targetPhotometric);
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
209
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
210 if (options.count(OPTION_JPEG_QUALITY))
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
211 {
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
212 target.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>());
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
213 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
214
167
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
215 LOG(WARNING) << "Source photometric interpretation: " << EnumerationToString(source.GetPhotometricInterpretation());
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
216 LOG(WARNING) << "Target photometric interpretation: " << EnumerationToString(targetPhotometric);
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
217
199
a1c265cb2174 replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 196
diff changeset
218 std::unique_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options));
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
219
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
220 for (unsigned int level = 0; level < source.GetLevelCount(); level++)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
221 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
222 LOG(WARNING) << "Creating level " << level << " of size "
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
223 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
224 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
225 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
226
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
227 for (unsigned int level = 0; level < source.GetLevelCount(); level++)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
228 {
163
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 157
diff changeset
229 LOG(WARNING) << std::string(reencode ? "Re-encoding" : "Transcoding")
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
230 << " level " << level;
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
231
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
232 unsigned int countX = OrthancWSI::CeilingDivision
217
20bc074ec19a Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 214
diff changeset
233 (source.GetLevelWidth(level), source.GetTileWidth(level));
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
234
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
235 unsigned int countY = OrthancWSI::CeilingDivision
217
20bc074ec19a Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 214
diff changeset
236 (source.GetLevelHeight(level), source.GetTileHeight(level));
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
237
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
238 for (unsigned int tileY = 0; tileY < countY; tileY++)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
239 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
240 for (unsigned int tileX = 0; tileX < countX; tileX++)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
241 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
242 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
243
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
244 bool missing = false;
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
245 bool success = true;
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
246
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
247 std::string tile;
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
248 OrthancWSI::ImageCompression compression;
167
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
249
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
250 if (source.ReadRawTile(tile, compression, level, tileX, tileY))
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
251 {
167
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
252 if (compression == OrthancWSI::ImageCompression_Jpeg)
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
253 {
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
254 // Transcoding of JPEG tiles
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
255 target.WriteRawTile(tile, compression, level, tileX, tileY);
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
256 }
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
257 else if (reencode)
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
258 {
199
a1c265cb2174 replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 196
diff changeset
259 std::unique_ptr<Orthanc::ImageAccessor> decoded;
167
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
260
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
261 if (compression == OrthancWSI::ImageCompression_None)
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
262 {
217
20bc074ec19a Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 214
diff changeset
263 decoded.reset(OrthancWSI::ImageToolbox::DecodeRawTile(
20bc074ec19a Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 214
diff changeset
264 tile, source.GetPixelFormat(),
20bc074ec19a Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 214
diff changeset
265 source.GetTileWidth(level), source.GetTileHeight(level)));
167
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
266 }
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
267 else
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
268 {
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
269 decoded.reset(OrthancWSI::ImageToolbox::DecodeTile(tile, compression));
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
270 }
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
271
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
272 target.EncodeTile(*decoded, level, tileX, tileY);
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
273 }
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
274 else
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
275 {
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
276 success = false; // Re-encoding is mandatory
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
277 }
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
278 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
279 else
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
280 {
167
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
281 // Unable to read the raw tile: The tile is missing (sparse tiling)
605247fc8758 Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 163
diff changeset
282 missing = true;
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
283 }
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
284
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
285 if (!success)
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
286 {
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
287 LOG(WARNING) << "Cannot transcode a DICOM image that is not encoded using JPEG (it is "
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
288 << OrthancWSI::EnumerationToString(compression)
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
289 << "), please use the --" << OPTION_REENCODE << "=1 option";
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
290 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
291 }
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
292
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
293 if (missing)
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
294 {
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
295 LOG(WARNING) << "Sparse tiling: Using an empty image for missing tile ("
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
296 << tileX << "," << tileY << ") at level " << level;
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
297 target.EncodeTile(*empty, level, tileX, tileY);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
298 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
299 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
300 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
301
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
302 target.Flush();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
303 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
304 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
305
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
306
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
307
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
308 int main(int argc, char* argv[])
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
309 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
310 OrthancWSI::ApplicationToolbox::GlobalInitialize();
93
14146ecd1688 Display version of the framework in the logs
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 69
diff changeset
311 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
312
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
313 int exitStatus = 0;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
314 boost::program_options::variables_map options;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
315
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
316 try
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
317 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
318 if (ParseParameters(exitStatus, options, argc, argv))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
319 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
320 Orthanc::WebServiceParameters params;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
321
125
7a3f4d580625 SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 115
diff changeset
322 OrthancWSI::ApplicationToolbox::SetupRestApi(params, options);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
323
196
b0bd22077cd8 sharing code with orthanc-stone
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 194
diff changeset
324 OrthancStone::OrthancHttpConnection orthanc(params);
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
325 OrthancWSI::DicomPyramid source(orthanc, options[OPTION_INPUT].as<std::string>(),
69
d529d9ce3c7e cache for DicomPyramidInstance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 61
diff changeset
326 false /* don't use cached metadata */);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
327
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
328 OrthancWSI::TiledPyramidStatistics stats(source);
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
329 Run(stats, options);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
330 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
331 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
332 catch (Orthanc::OrthancException& e)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
333 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
334 LOG(ERROR) << "Terminating on exception: " << e.What();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
335
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
336 if (options.count(OPTION_REENCODE) == 0)
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
337 {
128
788dd04b87f5 cleaning up options in DicomToTiff
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 125
diff changeset
338 LOG(ERROR) << "Consider using option \"--" << OPTION_REENCODE << "\"";
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
339 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
340
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
341 exitStatus = -1;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
342 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
343
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
344 OrthancWSI::ApplicationToolbox::GlobalFinalize();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
345
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
346 return exitStatus;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
347 }