Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 309:7020852a8fa9
updated year to 2024
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Fri, 22 Mar 2024 15:48:12 +0100 |
parents | fa734a851551 |
children | 0683312e21ba |
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 | |
309
7020852a8fa9
updated year to 2024
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
298
diff
changeset
|
5 * Copyright (C) 2017-2024 Osimis S.A., Belgium |
7020852a8fa9
updated year to 2024
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
298
diff
changeset
|
6 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
0 | 7 * |
8 * This program is free software: you can redistribute it and/or | |
9 * modify it under the terms of the GNU Affero General Public License | |
10 * as published by the Free Software Foundation, either version 3 of | |
11 * the License, or (at your option) any later version. | |
12 * | |
13 * This program is distributed in the hope that it will be useful, but | |
14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
16 * Affero General Public License for more details. | |
17 * | |
18 * You should have received a copy of the GNU Affero General Public License | |
19 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
20 **/ | |
21 | |
22 | |
23 #include "../Framework/Algorithms/ReconstructPyramidCommand.h" | |
24 #include "../Framework/Algorithms/TranscodeTileCommand.h" | |
25 #include "../Framework/DicomToolbox.h" | |
26 #include "../Framework/DicomizerParameters.h" | |
217
20bc074ec19a
Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
27 #include "../Framework/ImageToolbox.h" |
0 | 28 #include "../Framework/ImagedVolumeParameters.h" |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
29 #include "../Framework/Inputs/CytomineImage.h" |
0 | 30 #include "../Framework/Inputs/HierarchicalTiff.h" |
31 #include "../Framework/Inputs/OpenSlidePyramid.h" | |
298
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
32 #include "../Framework/Inputs/PlainTiff.h" |
0 | 33 #include "../Framework/Inputs/TiledJpegImage.h" |
34 #include "../Framework/Inputs/TiledPngImage.h" | |
35 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
151 | 36 #include "../Framework/MultiThreading/BagOfTasksProcessor.h" |
0 | 37 #include "../Framework/Outputs/DicomPyramidWriter.h" |
38 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
39 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
40 #include <Compatibility.h> // For std::unique_ptr |
192 | 41 #include <DicomParsing/FromDcmtkBridge.h> |
42 #include <Logging.h> | |
43 #include <OrthancException.h> | |
213
2a4e1f7de5ab
remove calls to deprecated classes of JsonCpp
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
199
diff
changeset
|
44 #include <Toolbox.h> |
192 | 45 #include <SystemToolbox.h> |
59
7a3853d51c45
Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
57
diff
changeset
|
46 |
0 | 47 #include "ApplicationToolbox.h" |
48 | |
49 #include <EmbeddedResources.h> | |
50 | |
51 #include <dcmtk/dcmdata/dcdeftag.h> | |
52 #include <dcmtk/dcmdata/dcuid.h> | |
53 #include <dcmtk/dcmdata/dcvrobow.h> | |
54 #include <dcmtk/dcmdata/dcvrat.h> | |
55 | |
56 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
57 static const char* OPTION_COLOR = "color"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
58 static const char* OPTION_COMPRESSION = "compression"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
59 static const char* OPTION_DATASET = "dataset"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
60 static const char* OPTION_FOLDER = "folder"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
61 static const char* OPTION_FOLDER_PATTERN = "folder-pattern"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
62 static const char* OPTION_HELP = "help"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
63 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
64 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
65 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
66 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
67 static const char* OPTION_INPUT = "input"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
68 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
69 static const char* OPTION_LEVELS = "levels"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
70 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
71 static const char* OPTION_MAX_SIZE = "max-size"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
72 static const char* OPTION_OFFSET_X = "offset-x"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
73 static const char* OPTION_OFFSET_Y = "offset-y"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
74 static const char* OPTION_OPENSLIDE = "openslide"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
75 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
76 static const char* OPTION_PYRAMID = "pyramid"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
77 static const char* OPTION_REENCODE = "reencode"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
78 static const char* OPTION_REPAINT = "repaint"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
79 static const char* OPTION_SAFETY = "safety"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
80 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
81 static const char* OPTION_SMOOTH = "smooth"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
82 static const char* OPTION_THREADS = "threads"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
83 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
84 static const char* OPTION_TILE_WIDTH = "tile-width"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
85 static const char* OPTION_VERBOSE = "verbose"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
86 static const char* OPTION_VERSION = "version"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
87 |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
88 // New in release 1.1 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
89 static const char* OPTION_CYTOMINE_URL = "cytomine-url"; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
90 static const char* OPTION_CYTOMINE_IMAGE_INSTANCE_ID = "cytomine-image"; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
91 static const char* OPTION_CYTOMINE_PUBLIC_KEY = "cytomine-public-key"; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
92 static const char* OPTION_CYTOMINE_PRIVATE_KEY = "cytomine-private-key"; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
93 static const char* OPTION_CYTOMINE_COMPRESSION = "cytomine-compression"; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
94 |
298
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
95 // New in release 2.1 |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
96 static const char* OPTION_TIFF_ALIGNMENT = "tiff-alignment"; |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
97 |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
98 |
226 | 99 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
100 | |
101 bool ReadJsonWithoutComments(Json::Value& target, | |
102 const std::string& source) | |
103 { | |
104 return Orthanc::Toolbox::ReadJsonWithoutComments(target, source); | |
105 } | |
106 | |
107 #else | |
108 | |
109 // Backward compatibility with Orthanc framework <= 1.8.2 | |
110 #include <json/reader.h> | |
111 | |
112 bool ReadJsonWithoutComments(Json::Value& target, | |
113 const std::string& source) | |
114 { | |
115 Json::Reader reader; | |
116 return reader.parse(source, target, false); | |
117 } | |
118 #endif | |
119 | |
120 | |
0 | 121 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
122 OrthancWSI::ITiledPyramid& source, | |
123 const OrthancWSI::DicomizerParameters& parameters) | |
124 { | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
125 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
|
126 |
236
b0ee417b667a
migrating new definitions in namespace Orthanc to namespace OrthancWSI
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
226
diff
changeset
|
127 OrthancWSI::BagOfTasks tasks; |
0 | 128 |
129 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
130 { | |
131 LOG(WARNING) << "Creating level " << i << " of size " | |
132 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
133 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
134 } | |
135 | |
136 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
137 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
138 } | |
139 | |
140 | |
141 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
142 OrthancWSI::ITiledPyramid& source, | |
143 const OrthancWSI::DicomizerParameters& parameters) | |
144 { | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
145 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
|
146 |
236
b0ee417b667a
migrating new definitions in namespace Orthanc to namespace OrthancWSI
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
226
diff
changeset
|
147 OrthancWSI::BagOfTasks tasks; |
0 | 148 |
149 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
150 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
151 assert(levelsCount >= 1); | |
152 | |
153 for (unsigned int i = 0; i < levelsCount; i++) | |
154 { | |
155 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
156 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
157 | |
158 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
159 target.AddLevel(width, height); | |
160 } | |
161 | |
162 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
163 if (lowerLevelsCount > levelsCount) | |
164 { | |
165 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
166 << ") exceeds the number of levels (" << levelsCount | |
167 << "), cropping it"; | |
168 lowerLevelsCount = levelsCount; | |
169 } | |
170 | |
171 assert(lowerLevelsCount <= levelsCount); | |
172 if (lowerLevelsCount != levelsCount) | |
173 { | |
174 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
|
175 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
0 | 176 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
177 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
178 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
179 | |
180 assert(tasks.GetSize() == 0); | |
181 | |
182 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
183 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
184 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
185 (tasks, target, truncated.GetUpperLevel(), | |
186 upperLevelsCount, lowerLevelsCount, parameters); | |
187 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
188 } | |
189 else | |
190 { | |
191 LOG(WARNING) << "Constructing the pyramid"; | |
192 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
193 (tasks, target, source, levelsCount, 0, parameters); | |
194 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
195 } | |
196 } | |
197 | |
198 | |
199 static void Recompress(OrthancWSI::IFileTarget& output, | |
200 OrthancWSI::ITiledPyramid& source, | |
201 const DcmDataset& dataset, | |
202 const OrthancWSI::DicomizerParameters& parameters, | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
203 const OrthancWSI::ImagedVolumeParameters& volume, |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
204 OrthancWSI::ImageCompression sourceCompression) |
0 | 205 { |
206 OrthancWSI::TiledPyramidStatistics stats(source); | |
207 | |
217
20bc074ec19a
Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
208 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); // Sanity check |
20bc074ec19a
Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
209 LOG(WARNING) << "Size of source tiles: " << stats.GetTileWidth(0) << "x" << stats.GetTileHeight(0); |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
210 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
211 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
|
212 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
0 | 213 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
214 | |
215 if (parameters.IsRepaintBackground()) | |
216 { | |
217 LOG(WARNING) << "Repainting the background with color: (" | |
218 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
219 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
220 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
221 } | |
222 else | |
223 { | |
224 LOG(WARNING) << "No repainting of the background"; | |
225 } | |
226 | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
227 Orthanc::PhotometricInterpretation targetPhotometric; |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
228 bool transcoding; |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
229 |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
230 if (parameters.IsForceReencode() || |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
231 parameters.IsReconstructPyramid() || |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
232 sourceCompression != parameters.GetTargetCompression()) |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
233 { |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
234 // 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
|
235 transcoding = false; |
171 | 236 |
237 if (source.GetPixelFormat() == Orthanc::PixelFormat_Grayscale8) | |
238 { | |
239 targetPhotometric = source.GetPhotometricInterpretation(); | |
240 } | |
241 else | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
242 { |
171 | 243 switch (parameters.GetTargetCompression()) |
244 { | |
245 case OrthancWSI::ImageCompression_Jpeg: | |
246 case OrthancWSI::ImageCompression_Jpeg2000: | |
247 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; | |
248 break; | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
249 |
171 | 250 case OrthancWSI::ImageCompression_None: |
251 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; | |
252 break; | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
253 |
171 | 254 default: |
255 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
256 } | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
257 } |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
258 } |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
259 else |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
260 { |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
261 // Transcoding: The tiles are copied (no re-encoding) |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
262 transcoding = true; |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
263 targetPhotometric = source.GetPhotometricInterpretation(); |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
264 } |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
265 |
0 | 266 OrthancWSI::DicomPyramidWriter target(output, dataset, |
267 source.GetPixelFormat(), | |
268 parameters.GetTargetCompression(), | |
269 parameters.GetTargetTileWidth(source), | |
270 parameters.GetTargetTileHeight(source), | |
271 parameters.GetDicomMaxFileSize(), | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
272 volume, targetPhotometric); |
29 | 273 target.SetJpegQuality(parameters.GetJpegQuality()); |
0 | 274 |
275 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
|
276 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
0 | 277 |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
278 if (!transcoding && |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
279 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
0 | 280 { |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
281 LOG(WARNING) << "Target compression: Jpeg with quality " |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
282 << static_cast<int>(target.GetJpegQuality()); |
0 | 283 target.SetJpegQuality(target.GetJpegQuality()); |
284 } | |
285 else | |
286 { | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
287 LOG(WARNING) << "Target compression: " |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
288 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
0 | 289 } |
290 | |
217
20bc074ec19a
Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
291 OrthancWSI::ImageToolbox::CheckConstantTileSize(stats); |
20bc074ec19a
Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
292 if (stats.GetTileWidth(0) % target.GetTileWidth() != 0 || |
20bc074ec19a
Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
293 stats.GetTileHeight(0) % target.GetTileHeight() != 0) |
0 | 294 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
295 LOG(ERROR) << "When resampling the tile size, " |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
296 << "it must be a integer divisor of the original tile size"; |
0 | 297 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
298 } | |
299 | |
300 if (target.GetTileWidth() <= 16 || | |
301 target.GetTileHeight() <= 16) | |
302 { | |
303 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
304 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
305 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
306 } | |
307 | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
308 if (transcoding) |
0 | 309 { |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
310 TranscodePyramid(target, stats, parameters); |
0 | 311 } |
312 else | |
313 { | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
314 ReconstructPyramid(target, stats, parameters); |
0 | 315 } |
316 | |
317 target.Flush(); | |
318 } | |
319 | |
320 | |
321 | |
322 static DcmDataset* ParseDataset(const std::string& path) | |
323 { | |
324 Json::Value json; | |
325 | |
326 if (path.empty()) | |
327 { | |
328 json = Json::objectValue; // Empty dataset => TODO EMBED | |
329 } | |
330 else | |
331 { | |
332 std::string content; | |
43 | 333 Orthanc::SystemToolbox::ReadFile(content, path); |
0 | 334 |
226 | 335 if (!ReadJsonWithoutComments(json, content)) |
0 | 336 { |
337 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
338 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
339 } | |
340 } | |
341 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
342 std::unique_ptr<DcmDataset> dataset(Orthanc::FromDcmtkBridge::FromJson(json, true, true, Orthanc::Encoding_Latin1, |
177
ea62c89b264b
fix due to change in the orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
175
diff
changeset
|
343 "" /* no private tag, thus no private creator */)); |
0 | 344 if (dataset.get() == NULL) |
345 { | |
346 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
347 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
348 } | |
349 | |
350 // VL Whole Slide Microscopy Image IOD | |
271
45e3b5adf4ae
opened issue 2379 in OpenSeadragon
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
265
diff
changeset
|
351 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, OrthancWSI::VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE_IOD); |
0 | 352 |
353 // Slide Microscopy | |
354 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
355 | |
356 // Patient orientation makes no sense in whole-slide images | |
357 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
358 | |
359 // Some basic coordinate information | |
360 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
361 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
362 | |
363 std::string date, time; | |
130 | 364 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
0 | 365 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
366 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
367 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
368 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
369 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
370 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
371 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
372 | |
373 return dataset.release(); | |
374 } | |
375 | |
376 | |
377 | |
378 static void SetupDimension(DcmDataset& dataset, | |
379 const std::string& opticalPathId, | |
380 const OrthancWSI::ITiledPyramid& source, | |
381 const OrthancWSI::ImagedVolumeParameters& volume) | |
382 { | |
83 | 383 // Extract the identifier of the Dimension Organization, if provided |
384 std::string organization; | |
0 | 385 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
386 | |
83 | 387 if (previous != NULL && |
388 previous->tagExists(DCM_DimensionOrganizationUID)) | |
389 { | |
390 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
391 } | |
392 else | |
0 | 393 { |
83 | 394 // No Dimension Organization provided: Generate an unique identifier |
395 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
396 } | |
397 | |
398 | |
399 { | |
400 // Construct tag "Dimension Organization Sequence" (0020,9221) | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
401 std::unique_ptr<DcmItem> item(new DcmItem); |
83 | 402 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
403 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
404 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); |
83 | 405 |
406 if (!sequence->insert(item.release(), false, false).good() || | |
407 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
0 | 408 { |
83 | 409 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
0 | 410 } |
411 } | |
412 | |
83 | 413 |
0 | 414 { |
83 | 415 // Construct tag "Dimension Index Sequence" (0020,9222) |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
416 std::unique_ptr<DcmItem> item(new DcmItem); |
83 | 417 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
|
418 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
|
419 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
|
420 |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
421 std::unique_ptr<DcmItem> item2(new DcmItem); |
84
727670c5c125
fix generation of "Dimension Index Sequence" and "Dimension Index Values"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
83
diff
changeset
|
422 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
|
423 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
|
424 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
0 | 425 |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
426 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
0 | 427 |
83 | 428 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
|
429 !sequence->insert(item2.release(), false, false).good() || |
83 | 430 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
431 { | |
432 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
433 } | |
0 | 434 } |
435 | |
436 | |
83 | 437 { |
438 // Construct tag "Shared Functional Groups Sequence" (5200,9229) | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
439 std::unique_ptr<DcmItem> item(new DcmItem); |
168
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
440 |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
441 std::unique_ptr<DcmItem> item3(new DcmItem); |
168
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
442 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
443 |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
444 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_SharedFunctionalGroupsSequence)); |
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
445 std::unique_ptr<DcmSequenceOfItems> sequence3(new DcmSequenceOfItems(DCM_OpticalPathIdentificationSequence)); |
168
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
446 |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
447 if (!sequence3->insert(item3.release(), false, false).good() || |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
448 !item->insert(sequence3.release(), false, false).good() || |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
449 !sequence->insert(item.release(), false, false).good() || |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
450 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
451 { |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
452 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
453 } |
0 | 454 } |
455 } | |
456 | |
457 | |
458 static void EnrichDataset(DcmDataset& dataset, | |
459 const OrthancWSI::ITiledPyramid& source, | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
460 OrthancWSI::ImageCompression sourceCompression, |
0 | 461 const OrthancWSI::DicomizerParameters& parameters, |
462 const OrthancWSI::ImagedVolumeParameters& volume) | |
463 { | |
464 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
465 | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
466 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
0 | 467 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
468 { | |
469 // Takes as estimation a 1:10 compression ratio | |
470 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
471 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
472 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
473 } | |
474 else | |
475 { | |
476 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
477 } | |
478 | |
479 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
480 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
481 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
482 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
483 std::unique_ptr<DcmItem> origin(new DcmItem); |
0 | 484 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, |
485 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
486 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
487 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
488 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
489 std::unique_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); |
0 | 490 if (!sequenceOrigin->insert(origin.release(), false, false).good() || |
491 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
492 { | |
493 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
494 } | |
495 | |
496 | |
497 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
498 { | |
499 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
500 { | |
501 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
502 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
503 } | |
504 | |
505 std::string brightfield; | |
506 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
507 | |
508 Json::Value json; | |
226 | 509 if (!ReadJsonWithoutComments(json, brightfield)) |
0 | 510 { |
511 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
512 } | |
513 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
514 std::unique_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( |
0 | 515 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), |
516 DCM_OpticalPathSequence.getElement()), | |
177
ea62c89b264b
fix due to change in the orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
175
diff
changeset
|
517 json, false, encoding, |
ea62c89b264b
fix due to change in the orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
175
diff
changeset
|
518 "" /* no private tag, thus no private creator */)); |
0 | 519 if (!dataset.insert(element.release()).good()) |
520 { | |
521 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
522 } | |
523 } | |
524 | |
525 | |
526 std::string profile; | |
527 if (parameters.GetIccProfilePath().empty()) | |
528 { | |
529 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
530 } | |
531 else | |
532 { | |
43 | 533 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
0 | 534 } |
535 | |
536 | |
537 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
538 if (opticalPath == NULL) | |
539 { | |
540 LOG(ERROR) << "No optical path specified"; | |
541 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
542 } | |
543 | |
544 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
545 { | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
546 std::unique_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); |
0 | 547 |
548 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
549 !opticalPath->insert(icc.release()).good()) | |
550 { | |
551 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
552 } | |
553 } | |
554 | |
555 const char* opticalPathId = NULL; | |
556 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
557 opticalPathId == NULL) | |
558 { | |
559 LOG(ERROR) << "No identifier in the optical path"; | |
560 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
561 } | |
562 | |
563 SetupDimension(dataset, opticalPathId, source, volume); | |
564 } | |
565 | |
566 | |
567 static bool ParseParameters(int& exitStatus, | |
568 OrthancWSI::DicomizerParameters& parameters, | |
569 OrthancWSI::ImagedVolumeParameters& volume, | |
570 int argc, | |
571 char* argv[]) | |
572 { | |
573 // Declare the supported parameters | |
574 boost::program_options::options_description generic("Generic options"); | |
575 generic.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
576 (OPTION_HELP, "Display this help and exit") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
577 (OPTION_VERSION, "Output version information and exit") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
578 (OPTION_VERBOSE, "Be verbose in logs") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
579 (OPTION_THREADS, |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
580 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
0 | 581 "Number of processing threads to be used") |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
582 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
583 "Path to the shared library of OpenSlide " |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
584 "(not necessary if converting from standard hierarchical TIFF)") |
0 | 585 ; |
586 | |
587 boost::program_options::options_description source("Options for the source image"); | |
588 source.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
589 (OPTION_DATASET, boost::program_options::value<std::string>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
590 "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
|
591 (OPTION_SAMPLE_DATASET, |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
592 "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
|
593 (OPTION_REENCODE, boost::program_options::value<bool>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
594 "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
|
595 (OPTION_REPAINT, boost::program_options::value<bool>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
596 "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
|
597 (OPTION_COLOR, boost::program_options::value<std::string>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
598 "Color of the background (e.g. \"255,0,0\")") |
298
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
599 (OPTION_TIFF_ALIGNMENT, boost::program_options::value<int>()->default_value(64), |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
600 "Add padding to plain TIFF images to align the width/height to multiples " |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
601 "of this value, very useful to enable deep zoom with IIIF (1 means no padding)") |
0 | 602 ; |
603 | |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
604 boost::program_options::options_description cytomine("Options if importing from Cytomine"); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
605 cytomine.add_options() |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
606 (OPTION_CYTOMINE_URL, boost::program_options::value<std::string>(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
607 "URL of the source Cytomine server, for instance: https://demo.cytomine.be/") |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
608 (OPTION_CYTOMINE_PUBLIC_KEY, boost::program_options::value<std::string>(), |
246 | 609 "Your personal public key in Cytomine (cf. Account in the Cytomine Web interface)") |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
610 (OPTION_CYTOMINE_PRIVATE_KEY, boost::program_options::value<std::string>(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
611 "Your personal private key in Cytomine (to be kept secret)") |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
612 (OPTION_CYTOMINE_IMAGE_INSTANCE_ID, boost::program_options::value<int>(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
613 "ID of the Image Instance of interest in Cytomine (must be an integer)") |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
614 (OPTION_CYTOMINE_COMPRESSION, boost::program_options::value<std::string>()->default_value("jpeg"), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
615 "Compression to be used for downloading the tiles from Cytomine, " |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
616 "can be \"jpeg\" (faster) or \"png\" (better quality)") |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
617 ; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
618 |
0 | 619 boost::program_options::options_description pyramid("Options to construct the pyramid"); |
620 pyramid.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
621 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
0 | 622 "Reconstruct the full pyramid (slow) (Boolean)") |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
623 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
0 | 624 "Apply smoothing when reconstructing the pyramid " |
625 "(slower, but higher quality) (Boolean)") | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
626 (OPTION_LEVELS, boost::program_options::value<int>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
627 "Number of levels in the target pyramid") |
0 | 628 ; |
629 | |
630 boost::program_options::options_description target("Options for the target image"); | |
631 target.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
632 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
633 "Width of the tiles in the target image") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
634 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
635 "Height of the tiles in the target image") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
636 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
0 | 637 "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
|
638 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
639 "Set quality level for JPEG (0..100)") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
640 (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
|
641 "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
|
642 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
0 | 643 "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
|
644 (OPTION_FOLDER_PATTERN, |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
645 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
0 | 646 "Pattern for the files in the output folder") |
647 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
648 "URL to the REST API of the target Orthanc server") | |
649 ; | |
650 | |
651 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
652 volumeOptions.add_options() | |
279
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
653 (OPTION_IMAGED_WIDTH, boost::program_options::value<float>(), |
289
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
654 "Width of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
279
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
655 (OPTION_IMAGED_HEIGHT, boost::program_options::value<float>(), |
289
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
656 "Height of the specimen (in mm), in the coordinate system of the glass slide, defaults to 15mm if missing") |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
657 (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
|
658 "Depth of the specimen (in mm)") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
659 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
0 | 660 "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
|
661 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
0 | 662 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
663 ; | |
664 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
665 boost::program_options::options_description restOptions |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
666 ("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
|
667 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
668 |
0 | 669 boost::program_options::options_description advancedOptions("Advanced options"); |
670 advancedOptions.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
671 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
0 | 672 "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
|
673 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
0 | 674 "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
|
675 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
0 | 676 "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
|
677 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
678 "Number of pyramid levels up to which multithreading " |
0 | 679 "should be applied (only for performance/memory tuning)") |
680 ; | |
681 | |
682 boost::program_options::options_description hidden; | |
683 hidden.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
684 (OPTION_INPUT, boost::program_options::value<std::string>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
685 "Input file"); |
0 | 686 ; |
687 | |
688 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
|
689 allWithoutHidden |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
690 .add(generic) |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
691 .add(source) |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
692 .add(cytomine) |
125
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
693 .add(pyramid) |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
694 .add(target) |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
695 .add(volumeOptions) |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
696 .add(restOptions) |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
697 .add(advancedOptions); |
0 | 698 |
699 boost::program_options::options_description all = allWithoutHidden; | |
700 all.add(hidden); | |
701 | |
702 boost::program_options::positional_options_description positional; | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
703 positional.add(OPTION_INPUT, 1); |
0 | 704 |
705 boost::program_options::variables_map options; | |
706 bool error = false; | |
707 | |
708 try | |
709 { | |
710 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
711 options(all).positional(positional).run(), options); | |
712 boost::program_options::notify(options); | |
713 } | |
714 catch (boost::program_options::error& e) | |
715 { | |
716 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
717 error = true; | |
718 } | |
719 | |
720 if (!error && | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
721 options.count(OPTION_SAMPLE_DATASET)) |
0 | 722 { |
723 std::string sample; | |
724 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
725 | |
726 std::cout << std::endl << sample << std::endl; | |
727 | |
728 return false; | |
729 } | |
730 | |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
731 // New in release 1.1 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
732 if (options.count(OPTION_CYTOMINE_URL) || |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
733 options.count(OPTION_CYTOMINE_PUBLIC_KEY) || |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
734 options.count(OPTION_CYTOMINE_PRIVATE_KEY) || |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
735 options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
736 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
737 if (!options.count(OPTION_CYTOMINE_URL)) |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
738 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
739 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
740 "URL to the Cytomine server is missing"); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
741 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
742 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
743 if (!options.count(OPTION_CYTOMINE_PUBLIC_KEY)) |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
744 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
745 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
746 "Public key for the Cytomine server is missing"); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
747 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
748 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
749 if (!options.count(OPTION_CYTOMINE_PRIVATE_KEY)) |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
750 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
751 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
752 "Private key for the Cytomine server is missing"); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
753 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
754 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
755 if (!options.count(OPTION_CYTOMINE_IMAGE_INSTANCE_ID)) |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
756 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
757 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
758 "The Image Instance ID from the Cytomine server is missing"); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
759 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
760 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
761 if (!options.count(OPTION_CYTOMINE_COMPRESSION)) |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
762 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
763 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
764 "The tile compression scheme for Cytomine is missing"); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
765 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
766 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
767 const std::string s = options[OPTION_CYTOMINE_COMPRESSION].as<std::string>(); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
768 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
769 OrthancWSI::ImageCompression compression; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
770 if (s == "jpeg") |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
771 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
772 compression = OrthancWSI::ImageCompression_Jpeg; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
773 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
774 else if (s == "png") |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
775 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
776 compression = OrthancWSI::ImageCompression_Png; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
777 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
778 else |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
779 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
780 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
781 "The tile compression scheme must be \"jpeg\" or \"png\", found: " + s); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
782 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
783 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
784 parameters.SetCytomineSource(options[OPTION_CYTOMINE_URL].as<std::string>(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
785 options[OPTION_CYTOMINE_PUBLIC_KEY].as<std::string>(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
786 options[OPTION_CYTOMINE_PRIVATE_KEY].as<std::string>(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
787 options[OPTION_CYTOMINE_IMAGE_INSTANCE_ID].as<int>(), compression); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
788 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
789 |
0 | 790 if (!error && |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
791 options.count(OPTION_HELP) == 0 && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
792 options.count(OPTION_VERSION) == 0 && |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
793 options.count(OPTION_INPUT) != 1 && |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
794 !parameters.IsCytomineSource()) |
0 | 795 { |
796 LOG(ERROR) << "No input file was specified"; | |
797 error = true; | |
798 } | |
799 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
800 if (error || options.count(OPTION_HELP)) |
0 | 801 { |
802 std::cout << std::endl | |
803 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
804 << std::endl | |
805 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
806 << std::endl << std::endl | |
807 << "Create a DICOM file from a digital pathology image." | |
808 << std::endl; | |
809 | |
810 std::cout << allWithoutHidden << "\n"; | |
811 | |
812 if (error) | |
813 { | |
814 exitStatus = -1; | |
815 } | |
816 | |
817 return false; | |
818 } | |
819 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
820 if (options.count(OPTION_VERSION)) |
8
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
821 { |
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
822 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
823 return false; |
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
824 } |
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
825 |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
826 if (options.count(OPTION_VERBOSE)) |
0 | 827 { |
828 Orthanc::Logging::EnableInfoLevel(true); | |
829 } | |
830 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
831 if (options.count(OPTION_OPENSLIDE)) |
0 | 832 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
833 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
0 | 834 } |
835 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
836 if (options.count(OPTION_PYRAMID) && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
837 options[OPTION_PYRAMID].as<bool>()) |
0 | 838 { |
839 parameters.SetReconstructPyramid(true); | |
840 } | |
841 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
842 if (options.count(OPTION_SMOOTH) && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
843 options[OPTION_SMOOTH].as<bool>()) |
0 | 844 { |
845 parameters.SetSmoothEnabled(true); | |
846 } | |
847 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
848 if (options.count(OPTION_SAFETY) && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
849 options[OPTION_SAFETY].as<bool>()) |
0 | 850 { |
851 parameters.SetSafetyCheck(true); | |
852 } | |
853 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
854 if (options.count(OPTION_REENCODE) && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
855 options[OPTION_REENCODE].as<bool>()) |
0 | 856 { |
857 parameters.SetForceReencode(true); | |
858 } | |
859 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
860 if (options.count(OPTION_REPAINT) && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
861 options[OPTION_REPAINT].as<bool>()) |
0 | 862 { |
863 parameters.SetRepaintBackground(true); | |
864 } | |
865 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
866 if (options.count(OPTION_TILE_WIDTH) || |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
867 options.count(OPTION_TILE_HEIGHT)) |
0 | 868 { |
869 int w = 0; | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
870 if (options.count(OPTION_TILE_WIDTH)) |
0 | 871 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
872 w = options[OPTION_TILE_WIDTH].as<int>(); |
0 | 873 } |
874 | |
145 | 875 int h = 0; |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
876 if (options.count(OPTION_TILE_HEIGHT)) |
0 | 877 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
878 h = options[OPTION_TILE_HEIGHT].as<int>(); |
0 | 879 } |
880 | |
881 if (w < 0 || h < 0) | |
882 { | |
883 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
884 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
885 } | |
886 | |
887 parameters.SetTargetTileSize(w, h); | |
888 } | |
889 | |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
890 if (!parameters.IsCytomineSource()) |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
891 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
892 parameters.SetInputFile(options[OPTION_INPUT].as<std::string>()); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
893 } |
0 | 894 |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
895 if (options.count(OPTION_COLOR)) |
0 | 896 { |
897 uint8_t r, g, b; | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
898 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
0 | 899 parameters.SetBackgroundColor(r, g, b); |
900 } | |
901 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
902 if (options.count(OPTION_COMPRESSION)) |
0 | 903 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
904 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
0 | 905 if (s == "none") |
906 { | |
907 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
908 } | |
909 else if (s == "jpeg") | |
910 { | |
911 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
912 } | |
913 else if (s == "jpeg2000") | |
914 { | |
915 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
916 } | |
917 else | |
918 { | |
919 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
920 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
921 } | |
922 } | |
923 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
924 if (options.count(OPTION_JPEG_QUALITY)) |
0 | 925 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
926 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>()); |
0 | 927 } |
928 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
929 if (options.count(OPTION_LEVELS)) |
0 | 930 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
931 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].as<int>()); |
0 | 932 } |
933 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
934 if (options.count(OPTION_LOWER_LEVELS)) |
0 | 935 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
936 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
0 | 937 } |
938 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
939 if (options.count(OPTION_THREADS)) |
0 | 940 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
941 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
0 | 942 } |
943 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
944 if (options.count(OPTION_MAX_SIZE)) |
0 | 945 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
946 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
0 | 947 } |
948 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
949 if (options.count(OPTION_FOLDER)) |
0 | 950 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
951 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
0 | 952 } |
953 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
954 if (options.count(OPTION_FOLDER_PATTERN)) |
0 | 955 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
956 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
0 | 957 } |
958 | |
125
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
959 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
0 | 960 |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
961 if (options.count(OPTION_DATASET)) |
0 | 962 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
963 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
0 | 964 } |
965 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
966 if (options.count(OPTION_IMAGED_WIDTH)) |
0 | 967 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
968 volume.SetWidth(options[OPTION_IMAGED_WIDTH].as<float>()); |
0 | 969 } |
970 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
971 if (options.count(OPTION_IMAGED_HEIGHT)) |
0 | 972 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
973 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].as<float>()); |
0 | 974 } |
975 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
976 if (options.count(OPTION_IMAGED_DEPTH)) |
0 | 977 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
978 volume.SetDepth(options[OPTION_IMAGED_DEPTH].as<float>()); |
0 | 979 } |
980 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
981 if (options.count(OPTION_OFFSET_X)) |
0 | 982 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
983 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
0 | 984 } |
985 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
986 if (options.count(OPTION_OFFSET_Y)) |
0 | 987 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
988 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
0 | 989 } |
990 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
991 if (options.count(OPTION_OPTICAL_PATH)) |
0 | 992 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
993 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
0 | 994 if (s == "none") |
995 { | |
996 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
997 } | |
998 else if (s == "brightfield") | |
999 { | |
1000 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
1001 } | |
1002 else | |
1003 { | |
1004 LOG(ERROR) << "Unknown optical path definition: " << s; | |
1005 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
1006 } | |
1007 } | |
1008 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
1009 if (options.count(OPTION_ICC_PROFILE)) |
0 | 1010 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
1011 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
0 | 1012 } |
1013 | |
298
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1014 if (options.count(OPTION_TIFF_ALIGNMENT)) |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1015 { |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1016 int value = options[OPTION_TIFF_ALIGNMENT].as<int>(); |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1017 if (value <= 0) |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1018 { |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1019 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1020 "TIFF alignment must be >= 1"); |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1021 } |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1022 else |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1023 { |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1024 parameters.SetTiffAlignment(static_cast<unsigned int>(value)); |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1025 } |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1026 } |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1027 |
0 | 1028 return true; |
1029 } | |
1030 | |
1031 | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
1032 |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1033 OrthancWSI::ITiledPyramid* OpenInputPyramid(OrthancWSI::ImageCompression& sourceCompression, |
279
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1034 OrthancWSI::ImagedVolumeParameters& volume, |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1035 const std::string& path, |
0 | 1036 const OrthancWSI::DicomizerParameters& parameters) |
1037 { | |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1038 if (parameters.IsCytomineSource()) |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1039 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1040 // New in release 1.1 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1041 LOG(WARNING) << "Importing Image Instance " << parameters.GetCytomineImageInstanceId() |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1042 << " from Cytomine server: " << parameters.GetCytomineServer().GetUrl(); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1043 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1044 return new OrthancWSI::CytomineImage(parameters.GetCytomineServer(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1045 parameters.GetCytominePublicKey(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1046 parameters.GetCytominePrivateKey(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1047 parameters.GetCytomineImageInstanceId(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1048 parameters.GetTargetTileWidth(512), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1049 parameters.GetTargetTileHeight(512)); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1050 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1051 |
0 | 1052 LOG(WARNING) << "The input image is: " << path; |
1053 | |
1054 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
1055 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
1056 | |
1057 switch (format) | |
1058 { | |
1059 case OrthancWSI::ImageCompression_Png: | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1060 { |
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1061 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 1062 return new OrthancWSI::TiledPngImage(path, |
1063 parameters.GetTargetTileWidth(512), | |
1064 parameters.GetTargetTileHeight(512)); | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1065 } |
0 | 1066 |
1067 case OrthancWSI::ImageCompression_Jpeg: | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1068 { |
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1069 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 1070 return new OrthancWSI::TiledJpegImage(path, |
1071 parameters.GetTargetTileWidth(512), | |
1072 parameters.GetTargetTileHeight(512)); | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1073 } |
0 | 1074 |
1075 case OrthancWSI::ImageCompression_Tiff: | |
1076 { | |
1077 try | |
1078 { | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
1079 std::unique_ptr<OrthancWSI::HierarchicalTiff> tiff(new OrthancWSI::HierarchicalTiff(path)); |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1080 sourceCompression = tiff->GetImageCompression(); |
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1081 return tiff.release(); |
0 | 1082 } |
1083 catch (Orthanc::OrthancException&) | |
1084 { | |
298
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1085 LOG(WARNING) << "This is not a standard hierarchical TIFF file, fallback to plain TIFF"; |
0 | 1086 } |
298
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1087 |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1088 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1089 return new OrthancWSI::PlainTiff(path, |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1090 parameters.GetTargetTileWidth(512), |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1091 parameters.GetTargetTileHeight(512), |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1092 parameters.GetTiffAlignment(), |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1093 parameters.GetBackgroundColorRed(), |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1094 parameters.GetBackgroundColorGreen(), |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1095 parameters.GetBackgroundColorBlue()); |
0 | 1096 } |
1097 | |
1098 default: | |
1099 break; | |
1100 } | |
1101 | |
1102 try | |
1103 { | |
1104 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
|
1105 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
279
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1106 |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1107 std::unique_ptr<OrthancWSI::OpenSlidePyramid> openslide( |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1108 new OrthancWSI::OpenSlidePyramid(path, parameters.GetTargetTileWidth(512), |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1109 parameters.GetTargetTileHeight(512))); |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1110 |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1111 float volumeWidth, volumeHeight; |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1112 if (openslide->LookupImagedVolumeSize(volumeWidth, volumeHeight)) |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1113 { |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1114 if (!volume.HasWidth()) |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1115 { |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1116 volume.SetWidth(volumeWidth); |
281 | 1117 LOG(WARNING) << "Width of the imaged volume extracted using OpenSlide: " << volumeWidth << "mm"; |
279
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1118 } |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1119 |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1120 if (!volume.HasHeight()) |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1121 { |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1122 volume.SetHeight(volumeHeight); |
281 | 1123 LOG(WARNING) << "Height of the imaged volume extracted using OpenSlide: " << volumeHeight << "mm"; |
279
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1124 } |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1125 } |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1126 |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1127 return openslide.release(); |
0 | 1128 } |
1129 catch (Orthanc::OrthancException&) | |
1130 { | |
1131 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
1132 return NULL; | |
1133 } | |
1134 } | |
1135 | |
1136 | |
1137 int main(int argc, char* argv[]) | |
1138 { | |
1139 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
93
14146ecd1688
Display version of the framework in the logs
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
84
diff
changeset
|
1140 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
0 | 1141 |
1142 int exitStatus = 0; | |
1143 | |
1144 try | |
1145 { | |
1146 OrthancWSI::DicomizerParameters parameters; | |
1147 OrthancWSI::ImagedVolumeParameters volume; | |
1148 | |
1149 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
1150 { | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1151 OrthancWSI::ImageCompression sourceCompression; |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
1152 std::unique_ptr<OrthancWSI::ITiledPyramid> source; |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1153 |
279
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1154 source.reset(OpenInputPyramid(sourceCompression, volume, parameters.GetInputFile(), parameters)); |
0 | 1155 if (source.get() == NULL) |
1156 { | |
1157 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
1158 } | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1159 |
289
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1160 // In the 2 lines below, remember to switch X/Y when going from physical to pixel coordinates! |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1161 float pixelSpacingX = volume.GetWidth() / static_cast<float>(source->GetLevelHeight(0)); |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1162 float pixelSpacingY = volume.GetHeight() / static_cast<float>(source->GetLevelWidth(0)); |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1163 if (std::abs(pixelSpacingX - pixelSpacingY) >= 100.0f * std::numeric_limits<float>::epsilon()) |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1164 { |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1165 LOG(WARNING) << "Your pixel spacing is different along the X and Y axes, make sure that " |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1166 << "you have not inversed the --" << OPTION_IMAGED_WIDTH << " and the --" |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1167 << OPTION_IMAGED_HEIGHT << " options: " << pixelSpacingX << " vs. " << pixelSpacingY; |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1168 } |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1169 |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1170 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
0 | 1171 |
1172 // Create the shared DICOM tags | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
1173 std::unique_ptr<DcmDataset> dataset(ParseDataset(parameters.GetDatasetPath())); |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1174 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
0 | 1175 |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
1176 std::unique_ptr<OrthancWSI::IFileTarget> output(parameters.CreateTarget()); |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
1177 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
0 | 1178 } |
1179 } | |
1180 catch (Orthanc::OrthancException& e) | |
1181 { | |
1182 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
1183 exitStatus = -1; | |
1184 } | |
1185 | |
1186 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
1187 | |
1188 return exitStatus; | |
1189 } |