Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 181:43b9c80594ed
back to mainline
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 26 May 2020 17:12:20 +0200 |
| parents | ea62c89b264b |
| children | f299c191cd76 |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
| 4 * Department, University Hospital of Liege, Belgium | |
|
175
e3cbf890b588
upgrade to year 2020
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
171
diff
changeset
|
5 * Copyright (C) 2017-2020 Osimis S.A., Belgium |
| 0 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 8 * modify it under the terms of the GNU Affero General Public License | |
| 9 * as published by the Free Software Foundation, either version 3 of | |
| 10 * the License, or (at your option) any later version. | |
| 11 * | |
| 12 * This program is distributed in the hope that it will be useful, but | |
| 13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 15 * Affero General Public License for more details. | |
| 16 * | |
| 17 * You should have received a copy of the GNU Affero General Public License | |
| 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 19 **/ | |
| 20 | |
| 21 | |
| 22 #include "../Framework/Algorithms/ReconstructPyramidCommand.h" | |
| 23 #include "../Framework/Algorithms/TranscodeTileCommand.h" | |
| 24 #include "../Framework/DicomToolbox.h" | |
| 25 #include "../Framework/DicomizerParameters.h" | |
| 26 #include "../Framework/ImagedVolumeParameters.h" | |
| 27 #include "../Framework/Inputs/HierarchicalTiff.h" | |
| 28 #include "../Framework/Inputs/OpenSlidePyramid.h" | |
| 29 #include "../Framework/Inputs/TiledJpegImage.h" | |
| 30 #include "../Framework/Inputs/TiledPngImage.h" | |
| 31 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
| 151 | 32 #include "../Framework/MultiThreading/BagOfTasksProcessor.h" |
| 0 | 33 #include "../Framework/Outputs/DicomPyramidWriter.h" |
| 34 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
| 35 | |
|
140
a0f9a3df1110
resort to Orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
130
diff
changeset
|
36 #include <Core/DicomParsing/FromDcmtkBridge.h> |
|
a0f9a3df1110
resort to Orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
130
diff
changeset
|
37 #include <Core/Logging.h> |
|
a0f9a3df1110
resort to Orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
130
diff
changeset
|
38 #include <Core/OrthancException.h> |
|
a0f9a3df1110
resort to Orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
130
diff
changeset
|
39 #include <Core/SystemToolbox.h> |
|
59
7a3853d51c45
Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
57
diff
changeset
|
40 |
| 0 | 41 #include "ApplicationToolbox.h" |
| 42 | |
| 43 #include <EmbeddedResources.h> | |
| 44 | |
| 45 #include <dcmtk/dcmdata/dcdeftag.h> | |
| 46 #include <dcmtk/dcmdata/dcuid.h> | |
| 47 #include <dcmtk/dcmdata/dcvrobow.h> | |
| 48 #include <dcmtk/dcmdata/dcvrat.h> | |
| 49 | |
| 50 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
51 static const char* OPTION_COLOR = "color"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
52 static const char* OPTION_COMPRESSION = "compression"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
53 static const char* OPTION_DATASET = "dataset"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
54 static const char* OPTION_FOLDER = "folder"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
55 static const char* OPTION_FOLDER_PATTERN = "folder-pattern"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
56 static const char* OPTION_HELP = "help"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
57 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
58 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
59 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
60 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
61 static const char* OPTION_INPUT = "input"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
62 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
63 static const char* OPTION_LEVELS = "levels"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
64 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
65 static const char* OPTION_MAX_SIZE = "max-size"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
66 static const char* OPTION_OFFSET_X = "offset-x"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
67 static const char* OPTION_OFFSET_Y = "offset-y"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
68 static const char* OPTION_OPENSLIDE = "openslide"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
69 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
70 static const char* OPTION_PYRAMID = "pyramid"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
71 static const char* OPTION_REENCODE = "reencode"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
72 static const char* OPTION_REPAINT = "repaint"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
73 static const char* OPTION_SAFETY = "safety"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
74 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
75 static const char* OPTION_SMOOTH = "smooth"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
76 static const char* OPTION_THREADS = "threads"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
77 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
78 static const char* OPTION_TILE_WIDTH = "tile-width"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
79 static const char* OPTION_VERBOSE = "verbose"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
80 static const char* OPTION_VERSION = "version"; |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
81 |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
82 |
| 0 | 83 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
| 84 OrthancWSI::ITiledPyramid& source, | |
| 85 const OrthancWSI::DicomizerParameters& parameters) | |
| 86 { | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
87 LOG(WARNING) << "Transcoding the source pyramid (not re-encoding)"; |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
88 |
| 0 | 89 Orthanc::BagOfTasks tasks; |
| 90 | |
| 91 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
| 92 { | |
| 93 LOG(WARNING) << "Creating level " << i << " of size " | |
| 94 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
| 95 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
| 96 } | |
| 97 | |
| 98 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
| 99 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 100 } | |
| 101 | |
| 102 | |
| 103 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
| 104 OrthancWSI::ITiledPyramid& source, | |
| 105 const OrthancWSI::DicomizerParameters& parameters) | |
| 106 { | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
107 LOG(WARNING) << "Re-encoding the source pyramid (not transcoding, slower process)"; |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
108 |
| 0 | 109 Orthanc::BagOfTasks tasks; |
| 110 | |
| 111 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
| 112 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
| 113 assert(levelsCount >= 1); | |
| 114 | |
| 115 for (unsigned int i = 0; i < levelsCount; i++) | |
| 116 { | |
| 117 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
| 118 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
| 119 | |
| 120 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
| 121 target.AddLevel(width, height); | |
| 122 } | |
| 123 | |
| 124 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
| 125 if (lowerLevelsCount > levelsCount) | |
| 126 { | |
| 127 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
| 128 << ") exceeds the number of levels (" << levelsCount | |
| 129 << "), cropping it"; | |
| 130 lowerLevelsCount = levelsCount; | |
| 131 } | |
| 132 | |
| 133 assert(lowerLevelsCount <= levelsCount); | |
| 134 if (lowerLevelsCount != levelsCount) | |
| 135 { | |
| 136 LOG(WARNING) << "Constructing the " << lowerLevelsCount << " lower levels of the pyramid"; | |
|
166
f0dac1e8f736
access to photometric interpretation of source pyramids
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
157
diff
changeset
|
137 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
| 0 | 138 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
| 139 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
| 140 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 141 | |
| 142 assert(tasks.GetSize() == 0); | |
| 143 | |
| 144 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
| 145 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
| 146 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 147 (tasks, target, truncated.GetUpperLevel(), | |
| 148 upperLevelsCount, lowerLevelsCount, parameters); | |
| 149 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 150 } | |
| 151 else | |
| 152 { | |
| 153 LOG(WARNING) << "Constructing the pyramid"; | |
| 154 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
| 155 (tasks, target, source, levelsCount, 0, parameters); | |
| 156 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
| 157 } | |
| 158 } | |
| 159 | |
| 160 | |
| 161 static void Recompress(OrthancWSI::IFileTarget& output, | |
| 162 OrthancWSI::ITiledPyramid& source, | |
| 163 const DcmDataset& dataset, | |
| 164 const OrthancWSI::DicomizerParameters& parameters, | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
165 const OrthancWSI::ImagedVolumeParameters& volume, |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
166 OrthancWSI::ImageCompression sourceCompression) |
| 0 | 167 { |
| 168 OrthancWSI::TiledPyramidStatistics stats(source); | |
| 169 | |
| 170 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth() << "x" << stats.GetTileHeight(); | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
171 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
172 LOG(WARNING) << "Source photometric interpretation: " << Orthanc::EnumerationToString(source.GetPhotometricInterpretation()); |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
173 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
| 0 | 174 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
| 175 | |
| 176 if (parameters.IsRepaintBackground()) | |
| 177 { | |
| 178 LOG(WARNING) << "Repainting the background with color: (" | |
| 179 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
| 180 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
| 181 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
| 182 } | |
| 183 else | |
| 184 { | |
| 185 LOG(WARNING) << "No repainting of the background"; | |
| 186 } | |
| 187 | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
188 Orthanc::PhotometricInterpretation targetPhotometric; |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
189 bool transcoding; |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
190 |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
191 if (parameters.IsForceReencode() || |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
192 parameters.IsReconstructPyramid() || |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
193 sourceCompression != parameters.GetTargetCompression()) |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
194 { |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
195 // The tiles of the source image will be re-encoded |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
196 transcoding = false; |
| 171 | 197 |
| 198 if (source.GetPixelFormat() == Orthanc::PixelFormat_Grayscale8) | |
| 199 { | |
| 200 targetPhotometric = source.GetPhotometricInterpretation(); | |
| 201 } | |
| 202 else | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
203 { |
| 171 | 204 switch (parameters.GetTargetCompression()) |
| 205 { | |
| 206 case OrthancWSI::ImageCompression_Jpeg: | |
| 207 case OrthancWSI::ImageCompression_Jpeg2000: | |
| 208 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; | |
| 209 break; | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
210 |
| 171 | 211 case OrthancWSI::ImageCompression_None: |
| 212 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; | |
| 213 break; | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
214 |
| 171 | 215 default: |
| 216 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 217 } | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
218 } |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
219 } |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
220 else |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
221 { |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
222 // Transcoding: The tiles are copied (no re-encoding) |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
223 transcoding = true; |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
224 targetPhotometric = source.GetPhotometricInterpretation(); |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
225 } |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
226 |
| 0 | 227 OrthancWSI::DicomPyramidWriter target(output, dataset, |
| 228 source.GetPixelFormat(), | |
| 229 parameters.GetTargetCompression(), | |
| 230 parameters.GetTargetTileWidth(source), | |
| 231 parameters.GetTargetTileHeight(source), | |
| 232 parameters.GetDicomMaxFileSize(), | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
233 volume, targetPhotometric); |
| 29 | 234 target.SetJpegQuality(parameters.GetJpegQuality()); |
| 0 | 235 |
| 236 LOG(WARNING) << "Size of target tiles: " << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
237 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
| 0 | 238 |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
239 if (!transcoding && |
|
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
240 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 0 | 241 { |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
242 LOG(WARNING) << "Target compression: Jpeg with quality " |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
243 << static_cast<int>(target.GetJpegQuality()); |
| 0 | 244 target.SetJpegQuality(target.GetJpegQuality()); |
| 245 } | |
| 246 else | |
| 247 { | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
248 LOG(WARNING) << "Target compression: " |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
249 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
| 0 | 250 } |
| 251 | |
| 252 if (stats.GetTileWidth() % target.GetTileWidth() != 0 || | |
| 253 stats.GetTileHeight() % target.GetTileHeight() != 0) | |
| 254 { | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
255 LOG(ERROR) << "When resampling the tile size, " |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
256 << "it must be a integer divisor of the original tile size"; |
| 0 | 257 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
| 258 } | |
| 259 | |
| 260 if (target.GetTileWidth() <= 16 || | |
| 261 target.GetTileHeight() <= 16) | |
| 262 { | |
| 263 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
| 264 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
| 265 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
| 266 } | |
| 267 | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
268 if (transcoding) |
| 0 | 269 { |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
270 TranscodePyramid(target, stats, parameters); |
| 0 | 271 } |
| 272 else | |
| 273 { | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
274 ReconstructPyramid(target, stats, parameters); |
| 0 | 275 } |
| 276 | |
| 277 target.Flush(); | |
| 278 } | |
| 279 | |
| 280 | |
| 281 | |
| 282 static DcmDataset* ParseDataset(const std::string& path) | |
| 283 { | |
| 284 Json::Value json; | |
| 285 | |
| 286 if (path.empty()) | |
| 287 { | |
| 288 json = Json::objectValue; // Empty dataset => TODO EMBED | |
| 289 } | |
| 290 else | |
| 291 { | |
| 292 std::string content; | |
| 43 | 293 Orthanc::SystemToolbox::ReadFile(content, path); |
| 0 | 294 |
| 295 Json::Reader reader; | |
| 296 if (!reader.parse(content, json, false)) | |
| 297 { | |
| 298 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
| 299 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 300 } | |
| 301 } | |
| 302 | |
|
177
ea62c89b264b
fix due to change in the orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
175
diff
changeset
|
303 std::auto_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1, |
|
ea62c89b264b
fix due to change in the orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
175
diff
changeset
|
304 "" /* no private tag, thus no private creator */)); |
| 0 | 305 if (dataset.get() == NULL) |
| 306 { | |
| 307 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
| 308 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 309 } | |
| 310 | |
| 311 // VL Whole Slide Microscopy Image IOD | |
| 312 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, "1.2.840.10008.5.1.4.1.1.77.1.6"); | |
| 313 | |
| 314 // Slide Microscopy | |
| 315 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
| 316 | |
| 317 // Patient orientation makes no sense in whole-slide images | |
| 318 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
| 319 | |
| 320 // Some basic coordinate information | |
| 321 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
| 322 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
| 323 | |
| 324 std::string date, time; | |
| 130 | 325 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
| 0 | 326 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
| 327 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
| 328 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
| 329 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
| 330 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
| 331 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
| 332 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
| 333 | |
| 334 return dataset.release(); | |
| 335 } | |
| 336 | |
| 337 | |
| 338 | |
| 339 static void SetupDimension(DcmDataset& dataset, | |
| 340 const std::string& opticalPathId, | |
| 341 const OrthancWSI::ITiledPyramid& source, | |
| 342 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 343 { | |
| 83 | 344 // Extract the identifier of the Dimension Organization, if provided |
| 345 std::string organization; | |
| 0 | 346 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
| 347 | |
| 83 | 348 if (previous != NULL && |
| 349 previous->tagExists(DCM_DimensionOrganizationUID)) | |
| 350 { | |
| 351 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
| 352 } | |
| 353 else | |
| 0 | 354 { |
| 83 | 355 // No Dimension Organization provided: Generate an unique identifier |
| 356 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
| 357 } | |
| 358 | |
| 359 | |
| 360 { | |
| 361 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
| 362 std::auto_ptr<DcmItem> item(new DcmItem); | |
| 363 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); | |
| 364 | |
| 365 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); | |
| 366 | |
| 367 if (!sequence->insert(item.release(), false, false).good() || | |
| 368 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
| 0 | 369 { |
| 83 | 370 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
| 0 | 371 } |
| 372 } | |
| 373 | |
| 83 | 374 |
| 0 | 375 { |
| 83 | 376 // Construct tag "Dimension Index Sequence" (0020,9222) |
| 377 std::auto_ptr<DcmItem> item(new DcmItem); | |
| 378 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
|
379 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
|
380 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
|
381 |
|
727670c5c125
fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
83
diff
changeset
|
382 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
|
383 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
|
384 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
|
385 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
| 0 | 386 |
| 83 | 387 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
| 0 | 388 |
| 83 | 389 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
|
390 !sequence->insert(item2.release(), false, false).good() || |
| 83 | 391 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
| 392 { | |
| 393 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 394 } | |
| 0 | 395 } |
| 396 | |
| 397 | |
| 83 | 398 { |
| 399 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
|
168
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
400 std::auto_ptr<DcmItem> item(new DcmItem); |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
401 |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
402 std::auto_ptr<DcmItem> item3(new DcmItem); |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
403 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
404 |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
405 std::auto_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
406 std::auto_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
407 |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
408 if (!sequence3->insert(item3.release(), false, false).good() || |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
409 !item->insert(sequence3.release(), false, false).good() || |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
410 !sequence->insert(item.release(), false, false).good() || |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
411 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
412 { |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
413 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
|
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
414 } |
| 0 | 415 } |
| 416 } | |
| 417 | |
| 418 | |
| 419 static void EnrichDataset(DcmDataset& dataset, | |
| 420 const OrthancWSI::ITiledPyramid& source, | |
|
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
421 OrthancWSI::ImageCompression sourceCompression, |
| 0 | 422 const OrthancWSI::DicomizerParameters& parameters, |
| 423 const OrthancWSI::ImagedVolumeParameters& volume) | |
| 424 { | |
| 425 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
| 426 | |
|
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
427 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
| 0 | 428 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
| 429 { | |
| 430 // Takes as estimation a 1:10 compression ratio | |
| 431 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
| 432 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
| 433 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
| 434 } | |
| 435 else | |
| 436 { | |
| 437 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
| 438 } | |
| 439 | |
| 440 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
| 441 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
| 442 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
| 443 | |
| 444 std::auto_ptr<DcmItem> origin(new DcmItem); | |
| 445 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, | |
| 446 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
| 447 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
| 448 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
| 449 | |
| 450 std::auto_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); | |
| 451 if (!sequenceOrigin->insert(origin.release(), false, false).good() || | |
| 452 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
| 453 { | |
| 454 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 455 } | |
| 456 | |
| 457 | |
| 458 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
| 459 { | |
| 460 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
| 461 { | |
| 462 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
| 463 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 464 } | |
| 465 | |
| 466 std::string brightfield; | |
| 467 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
| 468 | |
| 469 Json::Value json; | |
| 470 Json::Reader reader; | |
| 471 if (!reader.parse(brightfield, json, false)) | |
| 472 { | |
| 473 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 474 } | |
| 475 | |
| 476 std::auto_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( | |
| 477 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), | |
| 478 DCM_OpticalPathSequence.getElement()), | |
|
177
ea62c89b264b
fix due to change in the orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
175
diff
changeset
|
479 json, false, encoding, |
|
ea62c89b264b
fix due to change in the orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
175
diff
changeset
|
480 "" /* no private tag, thus no private creator */)); |
| 0 | 481 if (!dataset.insert(element.release()).good()) |
| 482 { | |
| 483 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 484 } | |
| 485 } | |
| 486 | |
| 487 | |
| 488 std::string profile; | |
| 489 if (parameters.GetIccProfilePath().empty()) | |
| 490 { | |
| 491 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
| 492 } | |
| 493 else | |
| 494 { | |
| 43 | 495 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
| 0 | 496 } |
| 497 | |
| 498 | |
| 499 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
| 500 if (opticalPath == NULL) | |
| 501 { | |
| 502 LOG(ERROR) << "No optical path specified"; | |
| 503 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 504 } | |
| 505 | |
| 506 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
| 507 { | |
| 508 std::auto_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); | |
| 509 | |
| 510 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
| 511 !opticalPath->insert(icc.release()).good()) | |
| 512 { | |
| 513 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 514 } | |
| 515 } | |
| 516 | |
| 517 const char* opticalPathId = NULL; | |
| 518 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
| 519 opticalPathId == NULL) | |
| 520 { | |
| 521 LOG(ERROR) << "No identifier in the optical path"; | |
| 522 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 523 } | |
| 524 | |
| 525 SetupDimension(dataset, opticalPathId, source, volume); | |
| 526 } | |
| 527 | |
| 528 | |
| 529 static bool ParseParameters(int& exitStatus, | |
| 530 OrthancWSI::DicomizerParameters& parameters, | |
| 531 OrthancWSI::ImagedVolumeParameters& volume, | |
| 532 int argc, | |
| 533 char* argv[]) | |
| 534 { | |
| 535 // Declare the supported parameters | |
| 536 boost::program_options::options_description generic("Generic options"); | |
| 537 generic.add_options() | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
538 (OPTION_HELP, "Display this help and exit") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
539 (OPTION_VERSION, "Output version information and exit") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
540 (OPTION_VERBOSE, "Be verbose in logs") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
541 (OPTION_THREADS, |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
542 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
| 0 | 543 "Number of processing threads to be used") |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
544 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
545 "Path to the shared library of OpenSlide " |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
546 "(not necessary if converting from standard hierarchical TIFF)") |
| 0 | 547 ; |
| 548 | |
| 549 boost::program_options::options_description source("Options for the source image"); | |
| 550 source.add_options() | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
551 (OPTION_DATASET, boost::program_options::value<std::string>(), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
552 "Path to a JSON file containing the DICOM dataset") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
553 (OPTION_SAMPLE_DATASET, |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
554 "Display a minimalistic sample DICOM dataset in JSON format, then exit") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
555 (OPTION_REENCODE, boost::program_options::value<bool>(), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
556 "Whether to re-encode each tile (no transcoding, much slower) (Boolean)") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
557 (OPTION_REPAINT, boost::program_options::value<bool>(), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
558 "Whether to repaint the background of the image (Boolean)") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
559 (OPTION_COLOR, boost::program_options::value<std::string>(), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
560 "Color of the background (e.g. \"255,0,0\")") |
| 0 | 561 ; |
| 562 | |
| 563 boost::program_options::options_description pyramid("Options to construct the pyramid"); | |
| 564 pyramid.add_options() | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
565 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
| 0 | 566 "Reconstruct the full pyramid (slow) (Boolean)") |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
567 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
| 0 | 568 "Apply smoothing when reconstructing the pyramid " |
| 569 "(slower, but higher quality) (Boolean)") | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
570 (OPTION_LEVELS, boost::program_options::value<int>(), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
571 "Number of levels in the target pyramid") |
| 0 | 572 ; |
| 573 | |
| 574 boost::program_options::options_description target("Options for the target image"); | |
| 575 target.add_options() | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
576 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
577 "Width of the tiles in the target image") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
578 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
579 "Height of the tiles in the target image") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
580 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
| 0 | 581 "Compression of the target image (\"none\", \"jpeg\" or \"jpeg2000\")") |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
582 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
583 "Set quality level for JPEG (0..100)") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
584 (OPTION_MAX_SIZE, boost::program_options::value<int>()->default_value(10), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
585 "Maximum size per DICOM instance (in MB), 0 means no limit on the file size") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
586 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
| 0 | 587 "Folder where to store the output DICOM instances") |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
588 (OPTION_FOLDER_PATTERN, |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
589 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
| 0 | 590 "Pattern for the files in the output folder") |
| 591 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
| 592 "URL to the REST API of the target Orthanc server") | |
| 593 ; | |
| 594 | |
| 595 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
| 596 volumeOptions.add_options() | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
597 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>()->default_value(15), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
598 "Width of the specimen (in mm)") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
599 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>()->default_value(15), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
600 "Height of the specimen (in mm)") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
601 (OPTION_IMAGED_DEPTH, boost::program_options::value<float>()->default_value(1), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
602 "Depth of the specimen (in mm)") |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
603 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
| 0 | 604 "X offset the specimen, wrt. slide coordinates origin (in mm)") |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
605 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
| 0 | 606 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
| 607 ; | |
| 608 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
609 boost::program_options::options_description restOptions |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
610 ("HTTP/HTTPS client configuration to access the Orthanc REST API"); |
|
125
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
611 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
|
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
612 |
| 0 | 613 boost::program_options::options_description advancedOptions("Advanced options"); |
| 614 advancedOptions.add_options() | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
615 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
| 0 | 616 "Optical path to be automatically added to the DICOM dataset (\"none\" or \"brightfield\")") |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
617 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
| 0 | 618 "Path to the ICC profile to be included. If empty, a default sRGB profile will be added.") |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
619 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
| 0 | 620 "Whether to do additional checks to verify the source image is supported (might slow down) (Boolean)") |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
621 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
622 "Number of pyramid levels up to which multithreading " |
| 0 | 623 "should be applied (only for performance/memory tuning)") |
| 624 ; | |
| 625 | |
| 626 boost::program_options::options_description hidden; | |
| 627 hidden.add_options() | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
628 (OPTION_INPUT, boost::program_options::value<std::string>(), |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
629 "Input file"); |
| 0 | 630 ; |
| 631 | |
| 632 boost::program_options::options_description allWithoutHidden; | |
|
125
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
633 allWithoutHidden |
|
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
634 .add(generic) |
|
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
635 .add(source) |
|
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
636 .add(pyramid) |
|
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
637 .add(target) |
|
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
638 .add(volumeOptions) |
|
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
639 .add(restOptions) |
|
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
640 .add(advancedOptions); |
| 0 | 641 |
| 642 boost::program_options::options_description all = allWithoutHidden; | |
| 643 all.add(hidden); | |
| 644 | |
| 645 boost::program_options::positional_options_description positional; | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
646 positional.add(OPTION_INPUT, 1); |
| 0 | 647 |
| 648 boost::program_options::variables_map options; | |
| 649 bool error = false; | |
| 650 | |
| 651 try | |
| 652 { | |
| 653 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
| 654 options(all).positional(positional).run(), options); | |
| 655 boost::program_options::notify(options); | |
| 656 } | |
| 657 catch (boost::program_options::error& e) | |
| 658 { | |
| 659 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
| 660 error = true; | |
| 661 } | |
| 662 | |
| 663 if (!error && | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
664 options.count(OPTION_SAMPLE_DATASET)) |
| 0 | 665 { |
| 666 std::string sample; | |
| 667 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
| 668 | |
| 669 std::cout << std::endl << sample << std::endl; | |
| 670 | |
| 671 return false; | |
| 672 } | |
| 673 | |
| 674 if (!error && | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
675 options.count(OPTION_HELP) == 0 && |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
676 options.count(OPTION_VERSION) == 0 && |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
677 options.count(OPTION_INPUT) != 1) |
| 0 | 678 { |
| 679 LOG(ERROR) << "No input file was specified"; | |
| 680 error = true; | |
| 681 } | |
| 682 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
683 if (error || options.count(OPTION_HELP)) |
| 0 | 684 { |
| 685 std::cout << std::endl | |
| 686 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
| 687 << std::endl | |
| 688 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
| 689 << std::endl << std::endl | |
| 690 << "Create a DICOM file from a digital pathology image." | |
| 691 << std::endl; | |
| 692 | |
| 693 std::cout << allWithoutHidden << "\n"; | |
| 694 | |
| 695 if (error) | |
| 696 { | |
| 697 exitStatus = -1; | |
| 698 } | |
| 699 | |
| 700 return false; | |
| 701 } | |
| 702 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
703 if (options.count(OPTION_VERSION)) |
|
8
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
704 { |
|
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
705 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
|
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
706 return false; |
|
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
707 } |
|
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
708 |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
709 if (options.count(OPTION_VERBOSE)) |
| 0 | 710 { |
| 711 Orthanc::Logging::EnableInfoLevel(true); | |
| 712 } | |
| 713 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
714 if (options.count(OPTION_OPENSLIDE)) |
| 0 | 715 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
716 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
| 0 | 717 } |
| 718 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
719 if (options.count(OPTION_PYRAMID) && |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
720 options[OPTION_PYRAMID].as<bool>()) |
| 0 | 721 { |
| 722 parameters.SetReconstructPyramid(true); | |
| 723 } | |
| 724 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
725 if (options.count(OPTION_SMOOTH) && |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
726 options[OPTION_SMOOTH].as<bool>()) |
| 0 | 727 { |
| 728 parameters.SetSmoothEnabled(true); | |
| 729 } | |
| 730 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
731 if (options.count(OPTION_SAFETY) && |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
732 options[OPTION_SAFETY].as<bool>()) |
| 0 | 733 { |
| 734 parameters.SetSafetyCheck(true); | |
| 735 } | |
| 736 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
737 if (options.count(OPTION_REENCODE) && |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
738 options[OPTION_REENCODE].as<bool>()) |
| 0 | 739 { |
| 740 parameters.SetForceReencode(true); | |
| 741 } | |
| 742 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
743 if (options.count(OPTION_REPAINT) && |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
744 options[OPTION_REPAINT].as<bool>()) |
| 0 | 745 { |
| 746 parameters.SetRepaintBackground(true); | |
| 747 } | |
| 748 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
749 if (options.count(OPTION_TILE_WIDTH) || |
|
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
750 options.count(OPTION_TILE_HEIGHT)) |
| 0 | 751 { |
| 752 int w = 0; | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
753 if (options.count(OPTION_TILE_WIDTH)) |
| 0 | 754 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
755 w = options[OPTION_TILE_WIDTH].as<int>(); |
| 0 | 756 } |
| 757 | |
| 145 | 758 int h = 0; |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
759 if (options.count(OPTION_TILE_HEIGHT)) |
| 0 | 760 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
761 h = options[OPTION_TILE_HEIGHT].as<int>(); |
| 0 | 762 } |
| 763 | |
| 764 if (w < 0 || h < 0) | |
| 765 { | |
| 766 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
| 767 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 768 } | |
| 769 | |
| 770 parameters.SetTargetTileSize(w, h); | |
| 771 } | |
| 772 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
773 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
| 0 | 774 |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
775 if (options.count(OPTION_COLOR)) |
| 0 | 776 { |
| 777 uint8_t r, g, b; | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
778 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
| 0 | 779 parameters.SetBackgroundColor(r, g, b); |
| 780 } | |
| 781 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
782 if (options.count(OPTION_COMPRESSION)) |
| 0 | 783 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
784 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
| 0 | 785 if (s == "none") |
| 786 { | |
| 787 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
| 788 } | |
| 789 else if (s == "jpeg") | |
| 790 { | |
| 791 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
| 792 } | |
| 793 else if (s == "jpeg2000") | |
| 794 { | |
| 795 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
| 796 } | |
| 797 else | |
| 798 { | |
| 799 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
| 800 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 801 } | |
| 802 } | |
| 803 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
804 if (options.count(OPTION_JPEG_QUALITY)) |
| 0 | 805 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
806 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
| 0 | 807 } |
| 808 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
809 if (options.count(OPTION_LEVELS)) |
| 0 | 810 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
811 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
| 0 | 812 } |
| 813 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
814 if (options.count(OPTION_LOWER_LEVELS)) |
| 0 | 815 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
816 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
| 0 | 817 } |
| 818 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
819 if (options.count(OPTION_THREADS)) |
| 0 | 820 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
821 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
| 0 | 822 } |
| 823 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
824 if (options.count(OPTION_MAX_SIZE)) |
| 0 | 825 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
826 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
| 0 | 827 } |
| 828 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
829 if (options.count(OPTION_FOLDER)) |
| 0 | 830 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
831 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
| 0 | 832 } |
| 833 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
834 if (options.count(OPTION_FOLDER_PATTERN)) |
| 0 | 835 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
836 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
| 0 | 837 } |
| 838 | |
|
125
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
839 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
| 0 | 840 |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
841 if (options.count(OPTION_DATASET)) |
| 0 | 842 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
843 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
| 0 | 844 } |
| 845 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
846 if (options.count(OPTION_IMAGED_WIDTH)) |
| 0 | 847 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
848 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
| 0 | 849 } |
| 850 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
851 if (options.count(OPTION_IMAGED_HEIGHT)) |
| 0 | 852 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
853 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
| 0 | 854 } |
| 855 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
856 if (options.count(OPTION_IMAGED_DEPTH)) |
| 0 | 857 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
858 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
| 0 | 859 } |
| 860 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
861 if (options.count(OPTION_OFFSET_X)) |
| 0 | 862 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
863 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
| 0 | 864 } |
| 865 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
866 if (options.count(OPTION_OFFSET_Y)) |
| 0 | 867 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
868 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
| 0 | 869 } |
| 870 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
871 if (options.count(OPTION_OPTICAL_PATH)) |
| 0 | 872 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
873 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
| 0 | 874 if (s == "none") |
| 875 { | |
| 876 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
| 877 } | |
| 878 else if (s == "brightfield") | |
| 879 { | |
| 880 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
| 881 } | |
| 882 else | |
| 883 { | |
| 884 LOG(ERROR) << "Unknown optical path definition: " << s; | |
| 885 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 886 } | |
| 887 } | |
| 888 | |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
889 if (options.count(OPTION_ICC_PROFILE)) |
| 0 | 890 { |
|
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
891 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
| 0 | 892 } |
| 893 | |
| 894 return true; | |
| 895 } | |
| 896 | |
| 897 | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
898 |
|
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
899 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
|
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
900 const std::string& path, |
| 0 | 901 const OrthancWSI::DicomizerParameters& parameters) |
| 902 { | |
| 903 LOG(WARNING) << "The input image is: " << path; | |
| 904 | |
| 905 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
| 906 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
| 907 | |
| 908 switch (format) | |
| 909 { | |
| 910 case OrthancWSI::ImageCompression_Png: | |
|
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
911 { |
|
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
912 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 913 return new OrthancWSI::TiledPngImage(path, |
| 914 parameters.GetTargetTileWidth(512), | |
| 915 parameters.GetTargetTileHeight(512)); | |
|
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
916 } |
| 0 | 917 |
| 918 case OrthancWSI::ImageCompression_Jpeg: | |
|
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
919 { |
|
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
920 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 921 return new OrthancWSI::TiledJpegImage(path, |
| 922 parameters.GetTargetTileWidth(512), | |
| 923 parameters.GetTargetTileHeight(512)); | |
|
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
924 } |
| 0 | 925 |
| 926 case OrthancWSI::ImageCompression_Tiff: | |
| 927 { | |
| 928 try | |
| 929 { | |
|
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
930 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
|
931 sourceCompression = tiff->GetImageCompression(); |
|
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
932 return tiff.release(); |
| 0 | 933 } |
| 934 catch (Orthanc::OrthancException&) | |
| 935 { | |
| 936 LOG(WARNING) << "This is not a standard hierarchical TIFF file"; | |
| 937 } | |
| 938 } | |
| 939 | |
| 940 default: | |
| 941 break; | |
| 942 } | |
| 943 | |
| 944 try | |
| 945 { | |
| 946 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
|
947 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
| 0 | 948 return new OrthancWSI::OpenSlidePyramid(path, |
| 949 parameters.GetTargetTileWidth(512), | |
| 950 parameters.GetTargetTileHeight(512)); | |
| 951 } | |
| 952 catch (Orthanc::OrthancException&) | |
| 953 { | |
| 954 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
| 955 return NULL; | |
| 956 } | |
| 957 } | |
| 958 | |
| 959 | |
| 960 int main(int argc, char* argv[]) | |
| 961 { | |
| 962 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
|
93
14146ecd1688
Display version of the framework in the logs
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
84
diff
changeset
|
963 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
| 0 | 964 |
| 965 int exitStatus = 0; | |
| 966 | |
| 967 try | |
| 968 { | |
| 969 OrthancWSI::DicomizerParameters parameters; | |
| 970 OrthancWSI::ImagedVolumeParameters volume; | |
| 971 | |
| 972 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
| 973 { | |
|
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
974 OrthancWSI::ImageCompression sourceCompression; |
|
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
975 std::auto_ptr<OrthancWSI::ITiledPyramid> source; |
|
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
976 |
|
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
977 source.reset(OpenInputPyramid(sourceCompression, parameters.GetInputFile(), parameters)); |
| 0 | 978 if (source.get() == NULL) |
| 979 { | |
| 980 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 981 } | |
|
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
982 |
|
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
983 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
| 0 | 984 |
| 985 // Create the shared DICOM tags | |
| 986 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
|
987 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
| 0 | 988 |
| 989 std::auto_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); | |
|
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
990 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
| 0 | 991 } |
| 992 } | |
| 993 catch (Orthanc::OrthancException& e) | |
| 994 { | |
| 995 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
| 996 exitStatus = -1; | |
| 997 } | |
| 998 | |
| 999 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
| 1000 | |
| 1001 return exitStatus; | |
| 1002 } |