annotate Applications/Dicomizer.cpp @ 106:18e9a5429cc4

clarification about --max-size option
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 19 Aug 2017 10:52:59 +0200
parents ff0ef01c332c
children a51dee6a1515
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
98
ff0ef01c332c shared copyright with osimis
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 93
diff changeset
5 * Copyright (C) 2017 Osimis, 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/Algorithms/ReconstructPyramidCommand.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
23 #include "../Framework/Algorithms/TranscodeTileCommand.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
24 #include "../Framework/DicomToolbox.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
25 #include "../Framework/DicomizerParameters.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
26 #include "../Framework/ImagedVolumeParameters.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
27 #include "../Framework/Inputs/HierarchicalTiff.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
28 #include "../Framework/Inputs/OpenSlidePyramid.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
29 #include "../Framework/Inputs/TiledJpegImage.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
30 #include "../Framework/Inputs/TiledPngImage.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
31 #include "../Framework/Inputs/TiledPyramidStatistics.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
32 #include "../Framework/Outputs/DicomPyramidWriter.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
33 #include "../Framework/Outputs/TruncatedPyramidWriter.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
34
59
7a3853d51c45 Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
35 #include "../Resources/Orthanc/Core/HttpClient.h"
7a3853d51c45 Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
36 #include "../Resources/Orthanc/Core/Logging.h"
7a3853d51c45 Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
37 #include "../Resources/Orthanc/Core/MultiThreading/BagOfTasksProcessor.h"
7a3853d51c45 Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
38 #include "../Resources/Orthanc/Core/SystemToolbox.h"
7a3853d51c45 Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
39 #include "../Resources/Orthanc/OrthancServer/FromDcmtkBridge.h"
7a3853d51c45 Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 57
diff changeset
40
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
41 #include "ApplicationToolbox.h"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
42
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
43 #include <EmbeddedResources.h>
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
44
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
45 #include <boost/program_options.hpp>
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
46
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
47 #include <dcmtk/dcmdata/dcdeftag.h>
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
48 #include <dcmtk/dcmdata/dcuid.h>
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
49 #include <dcmtk/dcmdata/dcvrobow.h>
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
50 #include <dcmtk/dcmdata/dcvrat.h>
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
51
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
52
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
53 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
54 OrthancWSI::ITiledPyramid& source,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
55 const OrthancWSI::DicomizerParameters& parameters)
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 Orthanc::BagOfTasks tasks;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
58
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
59 for (unsigned int i = 0; i < source.GetLevelCount(); i++)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
60 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
61 LOG(WARNING) << "Creating level " << i << " of size "
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
62 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
63 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i));
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
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
66 LOG(WARNING) << "Transcoding the source pyramid";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
67
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
68 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
69 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
70 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
71
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
72
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
73 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
74 OrthancWSI::ITiledPyramid& source,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
75 const OrthancWSI::DicomizerParameters& parameters)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
76 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
77 Orthanc::BagOfTasks tasks;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
78
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
79 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
80 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
81 assert(levelsCount >= 1);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
82
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
83 for (unsigned int i = 0; i < levelsCount; i++)
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 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
86 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i);
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 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
89 target.AddLevel(width, height);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
90 }
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 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
93 if (lowerLevelsCount > levelsCount)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
94 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
95 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
96 << ") exceeds the number of levels (" << levelsCount
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
97 << "), cropping it";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
98 lowerLevelsCount = levelsCount;
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
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
101 assert(lowerLevelsCount <= levelsCount);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
102 if (lowerLevelsCount != levelsCount)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
103 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
104 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
105 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
106 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
107 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
108 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
109
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
110 assert(tasks.GetSize() == 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 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
113 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
114 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
115 (tasks, target, truncated.GetUpperLevel(),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
116 upperLevelsCount, lowerLevelsCount, parameters);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
117 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
118 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
119 else
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 LOG(WARNING) << "Constructing the pyramid";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
122 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
123 (tasks, target, source, levelsCount, 0, parameters);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
124 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
125 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
126 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
127
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
128
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
129 static void Recompress(OrthancWSI::IFileTarget& output,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
130 OrthancWSI::ITiledPyramid& source,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
131 const DcmDataset& dataset,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
132 const OrthancWSI::DicomizerParameters& parameters,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
133 const OrthancWSI::ImagedVolumeParameters& volume)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
134 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
135 OrthancWSI::TiledPyramidStatistics stats(source);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
136
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
137 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth() << "x" << stats.GetTileHeight();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
138 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(stats.GetPixelFormat());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
139 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled");
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 if (parameters.IsRepaintBackground())
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 LOG(WARNING) << "Repainting the background with color: ("
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
144 << static_cast<int>(parameters.GetBackgroundColorRed()) << ","
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
145 << static_cast<int>(parameters.GetBackgroundColorGreen()) << ","
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
146 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
147 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
148 else
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
149 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
150 LOG(WARNING) << "No repainting of the background";
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
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
153 OrthancWSI::DicomPyramidWriter target(output, dataset,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
154 source.GetPixelFormat(),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
155 parameters.GetTargetCompression(),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
156 parameters.GetTargetTileWidth(source),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
157 parameters.GetTargetTileHeight(source),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
158 parameters.GetDicomMaxFileSize(),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
159 volume);
29
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 26
diff changeset
160 target.SetJpegQuality(parameters.GetJpegQuality());
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
161
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
162 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
163
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
164 if (target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
165 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
166 LOG(WARNING) << "Target image compression: Jpeg with quality " << static_cast<int>(target.GetJpegQuality());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
167 target.SetJpegQuality(target.GetJpegQuality());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
168 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
169 else
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
170 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
171 LOG(WARNING) << "Target image compression: " << OrthancWSI::EnumerationToString(target.GetImageCompression());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
172 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
173
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
174 if (stats.GetTileWidth() % target.GetTileWidth() != 0 ||
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
175 stats.GetTileHeight() % target.GetTileHeight() != 0)
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 LOG(ERROR) << "When resampling the tile size, it must be a integer divisor of the original tile size";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
178 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
179 }
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 if (target.GetTileWidth() <= 16 ||
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
182 target.GetTileHeight() <= 16)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
183 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
184 LOG(ERROR) << "Tiles are too small (16 pixels minimum): "
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
185 << target.GetTileWidth() << "x" << target.GetTileHeight();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
186 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
187 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
188
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
189 if (parameters.IsReconstructPyramid())
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
190 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
191 ReconstructPyramid(target, stats, parameters);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
192 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
193 else
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
194 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
195 TranscodePyramid(target, stats, parameters);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
196 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
197
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
198 target.Flush();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
199 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
200
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
201
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
202
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
203 static DcmDataset* ParseDataset(const std::string& path)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
204 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
205 Json::Value json;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
206
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
207 if (path.empty())
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
208 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
209 json = Json::objectValue; // Empty dataset => TODO EMBED
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
210 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
211 else
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
212 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
213 std::string content;
43
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
214 Orthanc::SystemToolbox::ReadFile(content, path);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
215
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
216 Json::Reader reader;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
217 if (!reader.parse(content, json, false))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
218 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
219 LOG(ERROR) << "Cannot parse the JSON file in: " << path;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
220 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
223
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
224 std::auto_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
225 if (dataset.get() == NULL)
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 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
228 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
229 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
230
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
231 // VL Whole Slide Microscopy Image IOD
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
232 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.77.1.6");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
233
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
234 // Slide Microscopy
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
235 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
236
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
237 // Patient orientation makes no sense in whole-slide images
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
238 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, "");
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 // Some basic coordinate information
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
241 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
242 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
243
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
244 std::string date, time;
43
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
245 Orthanc::SystemToolbox::GetNowDicom(date, time);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
246 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
247 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
248 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
249 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
250 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
251 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
252 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
253
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
254 return dataset.release();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
255 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
256
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
257
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
258
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
259 static void SetupDimension(DcmDataset& dataset,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
260 const std::string& opticalPathId,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
261 const OrthancWSI::ITiledPyramid& source,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
262 const OrthancWSI::ImagedVolumeParameters& volume)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
263 {
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
264 // Extract the identifier of the Dimension Organization, if provided
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
265 std::string organization;
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
266 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
267
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
268 if (previous != NULL &&
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
269 previous->tagExists(DCM_DimensionOrganizationUID))
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
270 {
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
271 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID);
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
272 }
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
273 else
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
274 {
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
275 // No Dimension Organization provided: Generate an unique identifier
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
276 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance);
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
277 }
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
278
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
279
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
280 {
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
281 // Construct tag "Dimension Organization Sequence" (0020,9221)
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
282 std::auto_ptr<DcmItem> item(new DcmItem);
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
283 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization);
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
284
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
285 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence));
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
286
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
287 if (!sequence->insert(item.release(), false, false).good() ||
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
288 !dataset.insert(sequence.release(), true /* replace */, false).good())
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
289 {
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
290 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
291 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
292 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
293
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
294
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
295 {
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
296 // Construct tag "Dimension Index Sequence" (0020,9222)
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
297 std::auto_ptr<DcmItem> item(new DcmItem);
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
298 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization);
84
727670c5c125 fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 83
diff changeset
299 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence);
727670c5c125 fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 83
diff changeset
300 OrthancWSI::DicomToolbox::SetAttributeTag(*item, DCM_DimensionIndexPointer, DCM_ColumnPositionInTotalImagePixelMatrix);
727670c5c125 fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 83
diff changeset
301
727670c5c125 fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 83
diff changeset
302 std::auto_ptr<DcmItem> item2(new DcmItem);
727670c5c125 fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 83
diff changeset
303 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_DimensionOrganizationUID, organization);
727670c5c125 fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 83
diff changeset
304 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_FunctionalGroupPointer, DCM_PlanePositionSlideSequence);
727670c5c125 fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 83
diff changeset
305 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
306
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
307 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence));
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
308
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
309 if (!sequence->insert(item.release(), false, false).good() ||
84
727670c5c125 fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 83
diff changeset
310 !sequence->insert(item2.release(), false, false).good() ||
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
311 !dataset.insert(sequence.release(), true /* replace */, false).good())
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
312 {
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
313 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
314 }
0
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
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
317
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
318 {
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
319 // Construct tag "Shared Functional Groups Sequence" (5200,9229)
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
320
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
321 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates!
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
322 float spacingX = volume.GetWidth() / static_cast<float>(source.GetLevelHeight(0));
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
323 float spacingY = volume.GetHeight() / static_cast<float>(source.GetLevelWidth(0));
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
324
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
325 std::string spacing = (boost::lexical_cast<std::string>(spacingX) + '\\' +
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
326 boost::lexical_cast<std::string>(spacingY));
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
327
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
328 std::auto_ptr<DcmItem> item(new DcmItem);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
329
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
330 std::auto_ptr<DcmItem> item2(new DcmItem);
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
331 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_SliceThickness,
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
332 boost::lexical_cast<std::string>(volume.GetDepth()));
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
333 OrthancWSI::DicomToolbox::SetStringTag(*item2, DCM_PixelSpacing, spacing);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
334
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
335 std::auto_ptr<DcmItem> item3(new DcmItem);
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
336 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
337
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
338 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence));
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
339 std::auto_ptr<DcmSequenceOfItems> sequence2(new DcmSequenceOfItems(DCM_PixelMeasuresSequence));
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
340 std::auto_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence));
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
341
83
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
342 if (!sequence2->insert(item2.release(), false, false).good() ||
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
343 !sequence3->insert(item3.release(), false, false).good() ||
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
344 !item->insert(sequence2.release(), false, false).good() ||
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
345 !item->insert(sequence3.release(), false, false).good() ||
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
346 !sequence->insert(item.release(), false, false).good() ||
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
347 !dataset.insert(sequence.release(), true /* replace */, false).good())
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
348 {
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
349 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
0cb3ac4f9159 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 59
diff changeset
350 }
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
351 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
352 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
353
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
354
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
355 static void EnrichDataset(DcmDataset& dataset,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
356 const OrthancWSI::ITiledPyramid& source,
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
357 OrthancWSI::ImageCompression sourceCompression,
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
358 const OrthancWSI::DicomizerParameters& parameters,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
359 const OrthancWSI::ImagedVolumeParameters& volume)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
360 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
361 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
362
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
363 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg ||
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
364 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
365 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
366 // Takes as estimation a 1:10 compression ratio
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
367 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
368 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
369 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
370 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
371 else
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
372 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
373 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
374 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
375
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
376 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth()));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
377 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight()));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
378 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth()));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
379
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
380 std::auto_ptr<DcmItem> origin(new DcmItem);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
381 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
382 boost::lexical_cast<std::string>(volume.GetOffsetX()));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
383 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
384 boost::lexical_cast<std::string>(volume.GetOffsetY()));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
385
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
386 std::auto_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
387 if (!sequenceOrigin->insert(origin.release(), false, false).good() ||
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
388 !dataset.insert(sequenceOrigin.release(), false, false).good())
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
389 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
390 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
391 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
392
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
393
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
394 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
395 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
396 if (dataset.tagExists(DCM_OpticalPathSequence))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
397 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
398 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
399 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
400 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
401
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
402 std::string brightfield;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
403 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
404
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
405 Json::Value json;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
406 Json::Reader reader;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
407 if (!reader.parse(brightfield, json, false))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
408 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
409 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
410 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
411
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
412 std::auto_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson(
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
413 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
414 DCM_OpticalPathSequence.getElement()),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
415 json, false, encoding));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
416 if (!dataset.insert(element.release()).good())
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
417 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
418 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
419 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
420 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
421
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
422
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
423 std::string profile;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
424 if (parameters.GetIccProfilePath().empty())
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
425 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
426 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
427 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
428 else
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
429 {
43
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 31
diff changeset
430 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath());
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
431 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
432
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
433
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
434 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
435 if (opticalPath == NULL)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
436 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
437 LOG(ERROR) << "No optical path specified";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
438 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
439 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
440
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
441 if (!opticalPath->tagExists(DCM_ICCProfile))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
442 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
443 std::auto_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
444
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
445 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() ||
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
446 !opticalPath->insert(icc.release()).good())
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
447 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
448 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
449 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
450 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
451
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
452 const char* opticalPathId = NULL;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
453 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() ||
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
454 opticalPathId == NULL)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
455 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
456 LOG(ERROR) << "No identifier in the optical path";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
457 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
458 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
459
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
460 SetupDimension(dataset, opticalPathId, source, volume);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
461 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
462
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
463
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
464 static bool ParseParameters(int& exitStatus,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
465 OrthancWSI::DicomizerParameters& parameters,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
466 OrthancWSI::ImagedVolumeParameters& volume,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
467 int argc,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
468 char* argv[])
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
469 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
470 // Declare the supported parameters
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
471 boost::program_options::options_description generic("Generic options");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
472 generic.add_options()
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
473 ("help", "Display this help and exit")
8
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
474 ("version", "Output version information and exit")
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
475 ("verbose", "Be verbose in logs")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
476 ("threads", boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
477 "Number of processing threads to be used")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
478 ("openslide", boost::program_options::value<std::string>(),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
479 "Path to the shared library of OpenSlide (not necessary if converting from standard hierarchical TIFF)")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
480 ;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
481
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
482 boost::program_options::options_description source("Options for the source image");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
483 source.add_options()
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
484 ("dataset", boost::program_options::value<std::string>(), "Path to a JSON file containing the DICOM dataset")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
485 ("sample-dataset", "Display a minimalistic sample DICOM dataset in JSON format, then exit")
31
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 29
diff changeset
486 ("reencode", boost::program_options::value<bool>(), "Whether to re-encode each tile (no transcoding, much slower) (Boolean)")
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
487 ("repaint", boost::program_options::value<bool>(), "Whether to repaint the background of the image (Boolean)")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
488 ("color", boost::program_options::value<std::string>(), "Color of the background (e.g. \"255,0,0\")")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
489 ;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
490
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
491 boost::program_options::options_description pyramid("Options to construct the pyramid");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
492 pyramid.add_options()
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
493 ("pyramid", boost::program_options::value<bool>()->default_value(false),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
494 "Reconstruct the full pyramid (slow) (Boolean)")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
495 ("smooth", boost::program_options::value<bool>()->default_value(false),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
496 "Apply smoothing when reconstructing the pyramid "
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
497 "(slower, but higher quality) (Boolean)")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
498 ("levels", boost::program_options::value<int>(), "Number of levels in the target pyramid")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
499 ;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
500
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
501 boost::program_options::options_description target("Options for the target image");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
502 target.add_options()
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
503 ("tile-width", boost::program_options::value<int>(), "Width of the tiles in the target image")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
504 ("tile-height", boost::program_options::value<int>(), "Height of the tiles in the target image")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
505 ("compression", boost::program_options::value<std::string>(),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
506 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
507 ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)")
106
18e9a5429cc4 clarification about --max-size option
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 98
diff changeset
508 ("max-size", boost::program_options::value<int>()->default_value(10), "Maximum size per DICOM instance (in MB), 0 means no limit on the file size")
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
509 ("folder", boost::program_options::value<std::string>(),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
510 "Folder where to store the output DICOM instances")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
511 ("folder-pattern", boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
512 "Pattern for the files in the output folder")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
513 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
514 "URL to the REST API of the target Orthanc server")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
515 ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
516 ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
517 ;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
518
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
519 boost::program_options::options_description volumeOptions("Description of the imaged volume");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
520 volumeOptions.add_options()
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
521 ("imaged-width", boost::program_options::value<float>()->default_value(15), "With of the specimen (in mm)")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
522 ("imaged-height", boost::program_options::value<float>()->default_value(15), "Height of the specimen (in mm)")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
523 ("imaged-depth", boost::program_options::value<float>()->default_value(1), "Depth of the specimen (in mm)")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
524 ("offset-x", boost::program_options::value<float>()->default_value(20),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
525 "X offset the specimen, wrt. slide coordinates origin (in mm)")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
526 ("offset-y", boost::program_options::value<float>()->default_value(40),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
527 "Y offset the specimen, wrt. slide coordinates origin (in mm)")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
528 ;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
529
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
530 boost::program_options::options_description advancedOptions("Advanced options");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
531 advancedOptions.add_options()
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
532 ("optical-path", boost::program_options::value<std::string>()->default_value("brightfield"),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
533 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
534 ("icc-profile", boost::program_options::value<std::string>(),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
535 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
536 ("safety", boost::program_options::value<bool>()->default_value(true),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
537 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
538 ("lower-levels", boost::program_options::value<int>(), "Number of pyramid levels up to which multithreading "
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
539 "should be applied (only for performance/memory tuning)")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
540 ;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
541
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
542 boost::program_options::options_description hidden;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
543 hidden.add_options()
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
544 ("input", boost::program_options::value<std::string>(), "Input file");
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
545 ;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
546
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
547 boost::program_options::options_description allWithoutHidden;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
548 allWithoutHidden.add(generic).add(source).add(pyramid).add(target).add(volumeOptions).add(advancedOptions);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
549
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
550 boost::program_options::options_description all = allWithoutHidden;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
551 all.add(hidden);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
552
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
553 boost::program_options::positional_options_description positional;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
554 positional.add("input", 1);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
555
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
556 boost::program_options::variables_map options;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
557 bool error = false;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
558
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
559 try
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
560 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
561 boost::program_options::store(boost::program_options::command_line_parser(argc, argv).
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
562 options(all).positional(positional).run(), options);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
563 boost::program_options::notify(options);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
564 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
565 catch (boost::program_options::error& e)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
566 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
567 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
568 error = true;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
569 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
570
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
571 if (!error &&
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
572 options.count("sample-dataset"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
573 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
574 std::string sample;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
575 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
576
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
577 std::cout << std::endl << sample << std::endl;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
578
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
579 return false;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
580 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
581
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
582 if (!error &&
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
583 options.count("help") == 0 &&
8
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
584 options.count("version") == 0 &&
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
585 options.count("input") != 1)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
586 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
587 LOG(ERROR) << "No input file was specified";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
588 error = true;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
589 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
590
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
591 if (error || options.count("help"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
592 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
593 std::cout << std::endl
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
594 << "Usage: " << argv[0] << " [OPTION]... [INPUT]"
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
595 << std::endl
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
596 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research."
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
597 << std::endl << std::endl
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
598 << "Create a DICOM file from a digital pathology image."
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
599 << std::endl;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
600
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
601 std::cout << allWithoutHidden << "\n";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
602
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
603 if (error)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
604 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
605 exitStatus = -1;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
606 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
607
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
608 return false;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
609 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
610
8
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
611 if (options.count("version"))
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
612 {
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
613 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]);
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
614 return false;
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
615 }
62adabb8c122 Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 0
diff changeset
616
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
617 if (options.count("verbose"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
618 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
619 Orthanc::Logging::EnableInfoLevel(true);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
620 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
621
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
622 if (options.count("openslide"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
623 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
624 OrthancWSI::OpenSlideLibrary::Initialize(options["openslide"].as<std::string>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
625 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
626
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
627 if (options.count("pyramid") &&
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
628 options["pyramid"].as<bool>())
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
629 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
630 parameters.SetReconstructPyramid(true);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
631 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
632
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
633 if (options.count("smooth") &&
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
634 options["smooth"].as<bool>())
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
635 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
636 parameters.SetSmoothEnabled(true);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
637 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
638
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
639 if (options.count("safety") &&
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
640 options["safety"].as<bool>())
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
641 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
642 parameters.SetSafetyCheck(true);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
643 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
644
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
645 if (options.count("reencode") &&
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
646 options["reencode"].as<bool>())
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
647 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
648 parameters.SetForceReencode(true);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
649 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
650
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
651 if (options.count("repaint") &&
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
652 options["repaint"].as<bool>())
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
653 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
654 parameters.SetRepaintBackground(true);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
655 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
656
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
657 if (options.count("tile-width") ||
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
658 options.count("tile-height"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
659 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
660 int w = 0;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
661 if (options.count("tile-width"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
662 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
663 w = options["tile-width"].as<int>();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
664 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
665
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
666 unsigned int h = 0;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
667 if (options.count("tile-height"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
668 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
669 h = options["tile-height"].as<int>();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
670 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
671
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
672 if (w < 0 || h < 0)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
673 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
674 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
675 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
676 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
677
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
678 parameters.SetTargetTileSize(w, h);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
679 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
680
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
681 parameters.SetInputFile(options["input"].as<std::string>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
682
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
683 if (options.count("color"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
684 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
685 uint8_t r, g, b;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
686 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options["color"].as<std::string>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
687 parameters.SetBackgroundColor(r, g, b);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
688 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
689
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
690 if (options.count("compression"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
691 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
692 std::string s = options["compression"].as<std::string>();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
693 if (s == "none")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
694 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
695 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
696 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
697 else if (s == "jpeg")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
698 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
699 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
700 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
701 else if (s == "jpeg2000")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
702 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
703 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
704 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
705 else
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
706 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
707 LOG(ERROR) << "Unknown image compression for the target image: " << s;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
708 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
709 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
710 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
711
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
712 if (options.count("jpeg-quality"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
713 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
714 parameters.SetJpegQuality(options["jpeg-quality"].as<int>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
715 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
716
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
717 if (options.count("levels"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
718 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
719 parameters.SetPyramidLevelsCount(options["levels"].as<int>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
720 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
721
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
722 if (options.count("lower-levels"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
723 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
724 parameters.SetPyramidLowerLevelsCount(options["lower-levels"].as<int>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
725 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
726
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
727 if (options.count("threads"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
728 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
729 parameters.SetThreadsCount(options["threads"].as<int>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
730 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
731
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
732 if (options.count("max-size"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
733 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
734 parameters.SetDicomMaxFileSize(options["max-size"].as<int>() * 1024 * 1024);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
735 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
736
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
737 if (options.count("folder"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
738 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
739 parameters.SetTargetFolder(options["folder"].as<std::string>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
740 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
741
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
742 if (options.count("folder-pattern"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
743 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
744 parameters.SetTargetFolderPattern(options["folder-pattern"].as<std::string>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
745 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
746
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
747 if (options.count("orthanc"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
748 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
749 parameters.GetOrthancParameters().SetUrl(options["orthanc"].as<std::string>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
750
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
751 if (options.count("username") &&
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
752 options.count("password"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
753 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
754 parameters.GetOrthancParameters().SetUsername(options["username"].as<std::string>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
755 parameters.GetOrthancParameters().SetPassword(options["password"].as<std::string>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
756 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
757 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
758
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
759 if (options.count("dataset"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
760 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
761 parameters.SetDatasetPath(options["dataset"].as<std::string>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
762 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
763
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
764 if (options.count("imaged-width"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
765 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
766 volume.SetWidth(options["imaged-width"].as<float>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
767 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
768
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
769 if (options.count("imaged-height"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
770 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
771 volume.SetHeight(options["imaged-height"].as<float>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
772 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
773
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
774 if (options.count("imaged-depth"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
775 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
776 volume.SetDepth(options["imaged-depth"].as<float>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
777 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
778
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
779 if (options.count("offset-x"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
780 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
781 volume.SetOffsetX(options["offset-x"].as<float>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
782 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
783
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
784 if (options.count("offset-y"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
785 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
786 volume.SetOffsetY(options["offset-y"].as<float>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
787 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
788
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
789 if (options.count("optical-path"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
790 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
791 std::string s = options["optical-path"].as<std::string>();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
792 if (s == "none")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
793 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
794 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
795 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
796 else if (s == "brightfield")
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
797 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
798 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
799 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
800 else
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
801 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
802 LOG(ERROR) << "Unknown optical path definition: " << s;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
803 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
804 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
805 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
806
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
807 if (options.count("icc-profile"))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
808 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
809 parameters.SetIccProfilePath(options["icc-profile"].as<std::string>());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
810 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
811
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
812 return true;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
813 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
814
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
815
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
816 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression,
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
817 const std::string& path,
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
818 const OrthancWSI::DicomizerParameters& parameters)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
819 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
820 LOG(WARNING) << "The input image is: " << path;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
821
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
822 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
823 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
824
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
825 switch (format)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
826 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
827 case OrthancWSI::ImageCompression_Png:
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
828 {
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
829 sourceCompression = OrthancWSI::ImageCompression_Unknown;
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
830 return new OrthancWSI::TiledPngImage(path,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
831 parameters.GetTargetTileWidth(512),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
832 parameters.GetTargetTileHeight(512));
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
833 }
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
834
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
835 case OrthancWSI::ImageCompression_Jpeg:
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
836 {
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
837 sourceCompression = OrthancWSI::ImageCompression_Unknown;
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
838 return new OrthancWSI::TiledJpegImage(path,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
839 parameters.GetTargetTileWidth(512),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
840 parameters.GetTargetTileHeight(512));
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
841 }
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
842
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
843 case OrthancWSI::ImageCompression_Tiff:
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
844 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
845 try
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
846 {
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
847 std::auto_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path));
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
848 sourceCompression = tiff->GetImageCompression();
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
849 return tiff.release();
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
850 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
851 catch (Orthanc::OrthancException&)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
852 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
853 LOG(WARNING) << "This is not a standard hierarchical TIFF file";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
854 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
855 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
856
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
857 default:
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
858 break;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
859 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
860
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
861 try
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
862 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
863 LOG(WARNING) << "Trying to open the input pyramid with OpenSlide";
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
864 sourceCompression = OrthancWSI::ImageCompression_Unknown;
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
865 return new OrthancWSI::OpenSlidePyramid(path,
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
866 parameters.GetTargetTileWidth(512),
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
867 parameters.GetTargetTileHeight(512));
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
868 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
869 catch (Orthanc::OrthancException&)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
870 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
871 LOG(ERROR) << "This file is not supported by OpenSlide";
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
872 return NULL;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
873 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
874 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
875
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
876
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
877 int main(int argc, char* argv[])
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
878 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
879 OrthancWSI::ApplicationToolbox::GlobalInitialize();
93
14146ecd1688 Display version of the framework in the logs
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 84
diff changeset
880 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
881
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
882 int exitStatus = 0;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
883
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
884 try
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
885 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
886 OrthancWSI::DicomizerParameters parameters;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
887 OrthancWSI::ImagedVolumeParameters volume;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
888
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
889 if (ParseParameters(exitStatus, parameters, volume, argc, argv))
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
890 {
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
891 OrthancWSI::ImageCompression sourceCompression;
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
892 std::auto_ptr<OrthancWSI::ITiledPyramid> source;
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
893
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
894 source.reset(OpenInputPyramid(sourceCompression, parameters.GetInputFile(), parameters));
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
895 if (source.get() == NULL)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
896 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
897 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
898 }
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
899
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
900 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
901
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
902 // Create the shared DICOM tags
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
903 std::auto_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath()));
57
91fc9583b2de big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 43
diff changeset
904 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume);
0
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
905
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
906 std::auto_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget());
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
907 Recompress(*output, *source, *dataset, parameters, volume);
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
908 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
909 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
910 catch (Orthanc::OrthancException& e)
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
911 {
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
912 LOG(ERROR) << "Terminating on exception: " << e.What();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
913 exitStatus = -1;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
914 }
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
915
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
916 OrthancWSI::ApplicationToolbox::GlobalFinalize();
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
917
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
918 return exitStatus;
4a7a53257c7d initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
919 }