Mercurial > hg > orthanc-wsi
annotate Applications/Dicomizer.cpp @ 324:a92bb720f90b
renamed option --tiff-alignment as --padding
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Wed, 16 Oct 2024 21:08:58 +0200 |
parents | 429c4efa1fde |
children | 9947e70cbcea |
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 | |
312
0683312e21ba
updated copyright, as Orthanc Team now replaces Osimis
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
309
diff
changeset
|
5 * Copyright (C) 2017-2023 Osimis S.A., Belgium |
0683312e21ba
updated copyright, as Orthanc Team now replaces Osimis
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
309
diff
changeset
|
6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium |
309
7020852a8fa9
updated year to 2024
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
298
diff
changeset
|
7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
0 | 8 * |
9 * This program is free software: you can redistribute it and/or | |
10 * modify it under the terms of the GNU Affero General Public License | |
11 * as published by the Free Software Foundation, either version 3 of | |
12 * the License, or (at your option) any later version. | |
13 * | |
14 * This program is distributed in the hope that it will be useful, but | |
15 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
17 * Affero General Public License for more details. | |
18 * | |
19 * You should have received a copy of the GNU Affero General Public License | |
20 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
21 **/ | |
22 | |
23 | |
24 #include "../Framework/Algorithms/ReconstructPyramidCommand.h" | |
25 #include "../Framework/Algorithms/TranscodeTileCommand.h" | |
26 #include "../Framework/DicomToolbox.h" | |
27 #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
|
28 #include "../Framework/ImageToolbox.h" |
0 | 29 #include "../Framework/ImagedVolumeParameters.h" |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
30 #include "../Framework/Inputs/CytomineImage.h" |
0 | 31 #include "../Framework/Inputs/HierarchicalTiff.h" |
32 #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
|
33 #include "../Framework/Inputs/PlainTiff.h" |
0 | 34 #include "../Framework/Inputs/TiledJpegImage.h" |
35 #include "../Framework/Inputs/TiledPngImage.h" | |
36 #include "../Framework/Inputs/TiledPyramidStatistics.h" | |
151 | 37 #include "../Framework/MultiThreading/BagOfTasksProcessor.h" |
0 | 38 #include "../Framework/Outputs/DicomPyramidWriter.h" |
39 #include "../Framework/Outputs/TruncatedPyramidWriter.h" | |
40 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
41 #include <Compatibility.h> // For std::unique_ptr |
192 | 42 #include <DicomParsing/FromDcmtkBridge.h> |
43 #include <Logging.h> | |
44 #include <OrthancException.h> | |
213
2a4e1f7de5ab
remove calls to deprecated classes of JsonCpp
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
199
diff
changeset
|
45 #include <Toolbox.h> |
192 | 46 #include <SystemToolbox.h> |
59
7a3853d51c45
Move "Framework/Orthanc/" as "Resources/Orthanc/"
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
57
diff
changeset
|
47 |
0 | 48 #include "ApplicationToolbox.h" |
49 | |
50 #include <EmbeddedResources.h> | |
51 | |
52 #include <dcmtk/dcmdata/dcdeftag.h> | |
53 #include <dcmtk/dcmdata/dcuid.h> | |
54 #include <dcmtk/dcmdata/dcvrobow.h> | |
55 #include <dcmtk/dcmdata/dcvrat.h> | |
56 | |
57 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
58 static const char* OPTION_COLOR = "color"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
59 static const char* OPTION_COMPRESSION = "compression"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
60 static const char* OPTION_DATASET = "dataset"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
61 static const char* OPTION_FOLDER = "folder"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
62 static const char* OPTION_FOLDER_PATTERN = "folder-pattern"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
63 static const char* OPTION_HELP = "help"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
64 static const char* OPTION_ICC_PROFILE = "icc-profile"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
65 static const char* OPTION_IMAGED_DEPTH = "imaged-depth"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
66 static const char* OPTION_IMAGED_HEIGHT = "imaged-height"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
67 static const char* OPTION_IMAGED_WIDTH = "imaged-width"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
68 static const char* OPTION_INPUT = "input"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
69 static const char* OPTION_JPEG_QUALITY = "jpeg-quality"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
70 static const char* OPTION_LEVELS = "levels"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
71 static const char* OPTION_LOWER_LEVELS = "lower-levels"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
72 static const char* OPTION_MAX_SIZE = "max-size"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
73 static const char* OPTION_OFFSET_X = "offset-x"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
74 static const char* OPTION_OFFSET_Y = "offset-y"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
75 static const char* OPTION_OPENSLIDE = "openslide"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
76 static const char* OPTION_OPTICAL_PATH = "optical-path"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
77 static const char* OPTION_PYRAMID = "pyramid"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
78 static const char* OPTION_REENCODE = "reencode"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
79 static const char* OPTION_REPAINT = "repaint"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
80 static const char* OPTION_SAFETY = "safety"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
81 static const char* OPTION_SAMPLE_DATASET = "sample-dataset"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
82 static const char* OPTION_SMOOTH = "smooth"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
83 static const char* OPTION_THREADS = "threads"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
84 static const char* OPTION_TILE_HEIGHT = "tile-height"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
85 static const char* OPTION_TILE_WIDTH = "tile-width"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
86 static const char* OPTION_VERBOSE = "verbose"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
87 static const char* OPTION_VERSION = "version"; |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
88 |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
89 // New in release 1.1 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
90 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
|
91 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
|
92 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
|
93 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
|
94 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
|
95 |
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
|
96 // New in release 2.1 |
324
a92bb720f90b
renamed option --tiff-alignment as --padding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
323
diff
changeset
|
97 static const char* OPTION_FORCE_OPENSLIDE = "force-openslide"; |
a92bb720f90b
renamed option --tiff-alignment as --padding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
323
diff
changeset
|
98 static const char* OPTION_PADDING = "padding"; |
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
|
99 |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
100 |
226 | 101 #if ORTHANC_FRAMEWORK_VERSION_IS_ABOVE(1, 9, 0) |
102 | |
103 bool ReadJsonWithoutComments(Json::Value& target, | |
104 const std::string& source) | |
105 { | |
106 return Orthanc::Toolbox::ReadJsonWithoutComments(target, source); | |
107 } | |
108 | |
109 #else | |
110 | |
111 // Backward compatibility with Orthanc framework <= 1.8.2 | |
112 #include <json/reader.h> | |
113 | |
114 bool ReadJsonWithoutComments(Json::Value& target, | |
115 const std::string& source) | |
116 { | |
117 Json::Reader reader; | |
118 return reader.parse(source, target, false); | |
119 } | |
120 #endif | |
121 | |
122 | |
0 | 123 static void TranscodePyramid(OrthancWSI::PyramidWriterBase& target, |
124 OrthancWSI::ITiledPyramid& source, | |
125 const OrthancWSI::DicomizerParameters& parameters) | |
126 { | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
127 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
|
128 |
236
b0ee417b667a
migrating new definitions in namespace Orthanc to namespace OrthancWSI
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
226
diff
changeset
|
129 OrthancWSI::BagOfTasks tasks; |
0 | 130 |
131 for (unsigned int i = 0; i < source.GetLevelCount(); i++) | |
132 { | |
133 LOG(WARNING) << "Creating level " << i << " of size " | |
134 << source.GetLevelWidth(i) << "x" << source.GetLevelHeight(i); | |
135 target.AddLevel(source.GetLevelWidth(i), source.GetLevelHeight(i)); | |
136 } | |
137 | |
138 OrthancWSI::TranscodeTileCommand::PrepareBagOfTasks(tasks, target, source, parameters); | |
139 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
140 } | |
141 | |
142 | |
143 static void ReconstructPyramid(OrthancWSI::PyramidWriterBase& target, | |
144 OrthancWSI::ITiledPyramid& source, | |
145 const OrthancWSI::DicomizerParameters& parameters) | |
146 { | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
147 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
|
148 |
236
b0ee417b667a
migrating new definitions in namespace Orthanc to namespace OrthancWSI
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
226
diff
changeset
|
149 OrthancWSI::BagOfTasks tasks; |
0 | 150 |
151 unsigned int levelsCount = parameters.GetPyramidLevelsCount(target, source); | |
152 LOG(WARNING) << "The target pyramid will have " << levelsCount << " levels"; | |
153 assert(levelsCount >= 1); | |
154 | |
155 for (unsigned int i = 0; i < levelsCount; i++) | |
156 { | |
157 unsigned int width = OrthancWSI::CeilingDivision(source.GetLevelWidth(0), 1 << i); | |
158 unsigned int height = OrthancWSI::CeilingDivision(source.GetLevelHeight(0), 1 << i); | |
159 | |
160 LOG(WARNING) << "Creating level " << i << " of size " << width << "x" << height; | |
161 target.AddLevel(width, height); | |
162 } | |
163 | |
164 unsigned int lowerLevelsCount = parameters.GetPyramidLowerLevelsCount(target, source); | |
165 if (lowerLevelsCount > levelsCount) | |
166 { | |
167 LOG(WARNING) << "The number of lower levels (" << lowerLevelsCount | |
168 << ") exceeds the number of levels (" << levelsCount | |
169 << "), cropping it"; | |
170 lowerLevelsCount = levelsCount; | |
171 } | |
172 | |
173 assert(lowerLevelsCount <= levelsCount); | |
174 if (lowerLevelsCount != levelsCount) | |
175 { | |
176 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
|
177 OrthancWSI::TruncatedPyramidWriter truncated(target, lowerLevelsCount, source.GetPhotometricInterpretation()); |
0 | 178 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks |
179 (tasks, truncated, source, lowerLevelsCount + 1, 0, parameters); | |
180 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
181 | |
182 assert(tasks.GetSize() == 0); | |
183 | |
184 const unsigned int upperLevelsCount = levelsCount - lowerLevelsCount; | |
185 LOG(WARNING) << "Constructing the " << upperLevelsCount << " upper levels of the pyramid"; | |
186 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
187 (tasks, target, truncated.GetUpperLevel(), | |
188 upperLevelsCount, lowerLevelsCount, parameters); | |
189 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
190 } | |
191 else | |
192 { | |
193 LOG(WARNING) << "Constructing the pyramid"; | |
194 OrthancWSI::ReconstructPyramidCommand::PrepareBagOfTasks | |
195 (tasks, target, source, levelsCount, 0, parameters); | |
196 OrthancWSI::ApplicationToolbox::Execute(tasks, parameters.GetThreadsCount()); | |
197 } | |
198 } | |
199 | |
200 | |
201 static void Recompress(OrthancWSI::IFileTarget& output, | |
202 OrthancWSI::ITiledPyramid& source, | |
203 const DcmDataset& dataset, | |
204 const OrthancWSI::DicomizerParameters& parameters, | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
205 const OrthancWSI::ImagedVolumeParameters& volume, |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
206 OrthancWSI::ImageCompression sourceCompression) |
0 | 207 { |
208 OrthancWSI::TiledPyramidStatistics stats(source); | |
209 | |
217
20bc074ec19a
Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
210 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
|
211 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
|
212 LOG(WARNING) << "Pixel format: " << Orthanc::EnumerationToString(source.GetPixelFormat()); |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
213 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
|
214 LOG(WARNING) << "Source compression: " << EnumerationToString(sourceCompression); |
0 | 215 LOG(WARNING) << "Smoothing is " << (parameters.IsSmoothEnabled() ? "enabled" : "disabled"); |
216 | |
217 if (parameters.IsRepaintBackground()) | |
218 { | |
219 LOG(WARNING) << "Repainting the background with color: (" | |
220 << static_cast<int>(parameters.GetBackgroundColorRed()) << "," | |
221 << static_cast<int>(parameters.GetBackgroundColorGreen()) << "," | |
222 << static_cast<int>(parameters.GetBackgroundColorBlue()) << ")"; | |
223 } | |
224 else | |
225 { | |
226 LOG(WARNING) << "No repainting of the background"; | |
227 } | |
228 | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
229 Orthanc::PhotometricInterpretation targetPhotometric; |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
230 bool transcoding; |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
231 |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
232 if (parameters.IsForceReencode() || |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
233 parameters.IsReconstructPyramid() || |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
234 sourceCompression != parameters.GetTargetCompression()) |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
235 { |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
236 // 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
|
237 transcoding = false; |
171 | 238 |
239 if (source.GetPixelFormat() == Orthanc::PixelFormat_Grayscale8) | |
240 { | |
241 targetPhotometric = source.GetPhotometricInterpretation(); | |
242 } | |
243 else | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
244 { |
171 | 245 switch (parameters.GetTargetCompression()) |
246 { | |
247 case OrthancWSI::ImageCompression_Jpeg: | |
248 case OrthancWSI::ImageCompression_Jpeg2000: | |
249 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422; | |
250 break; | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
251 |
171 | 252 case OrthancWSI::ImageCompression_None: |
253 targetPhotometric = Orthanc::PhotometricInterpretation_RGB; | |
254 break; | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
255 |
171 | 256 default: |
257 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
258 } | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
259 } |
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 else |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
262 { |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
263 // Transcoding: The tiles are copied (no re-encoding) |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
264 transcoding = true; |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
265 targetPhotometric = source.GetPhotometricInterpretation(); |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
266 } |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
267 |
0 | 268 OrthancWSI::DicomPyramidWriter target(output, dataset, |
269 source.GetPixelFormat(), | |
270 parameters.GetTargetCompression(), | |
271 parameters.GetTargetTileWidth(source), | |
272 parameters.GetTargetTileHeight(source), | |
273 parameters.GetDicomMaxFileSize(), | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
274 volume, targetPhotometric); |
29 | 275 target.SetJpegQuality(parameters.GetJpegQuality()); |
0 | 276 |
277 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
|
278 LOG(WARNING) << "Target photometric interpretation: " << Orthanc::EnumerationToString(targetPhotometric); |
0 | 279 |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
280 if (!transcoding && |
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
281 target.GetImageCompression() == OrthancWSI::ImageCompression_Jpeg) |
0 | 282 { |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
283 LOG(WARNING) << "Target compression: Jpeg with quality " |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
284 << static_cast<int>(target.GetJpegQuality()); |
0 | 285 target.SetJpegQuality(target.GetJpegQuality()); |
286 } | |
287 else | |
288 { | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
289 LOG(WARNING) << "Target compression: " |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
290 << OrthancWSI::EnumerationToString(target.GetImageCompression()); |
0 | 291 } |
292 | |
217
20bc074ec19a
Viewer can display DICOM pyramids whose tile sizes vary across levels
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
214
diff
changeset
|
293 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
|
294 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
|
295 stats.GetTileHeight(0) % target.GetTileHeight() != 0) |
0 | 296 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
297 LOG(ERROR) << "When resampling the tile size, " |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
298 << "it must be a integer divisor of the original tile size"; |
0 | 299 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); |
300 } | |
301 | |
302 if (target.GetTileWidth() <= 16 || | |
303 target.GetTileHeight() <= 16) | |
304 { | |
305 LOG(ERROR) << "Tiles are too small (16 pixels minimum): " | |
306 << target.GetTileWidth() << "x" << target.GetTileHeight(); | |
307 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize); | |
308 } | |
309 | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
310 if (transcoding) |
0 | 311 { |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
312 TranscodePyramid(target, stats, parameters); |
0 | 313 } |
314 else | |
315 { | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
316 ReconstructPyramid(target, stats, parameters); |
0 | 317 } |
318 | |
319 target.Flush(); | |
320 } | |
321 | |
322 | |
323 | |
324 static DcmDataset* ParseDataset(const std::string& path) | |
325 { | |
326 Json::Value json; | |
327 | |
328 if (path.empty()) | |
329 { | |
330 json = Json::objectValue; // Empty dataset => TODO EMBED | |
331 } | |
332 else | |
333 { | |
334 std::string content; | |
43 | 335 Orthanc::SystemToolbox::ReadFile(content, path); |
0 | 336 |
226 | 337 if (!ReadJsonWithoutComments(json, content)) |
0 | 338 { |
339 LOG(ERROR) << "Cannot parse the JSON file in: " << path; | |
340 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
341 } | |
342 } | |
343 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
344 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
|
345 "" /* no private tag, thus no private creator */)); |
0 | 346 if (dataset.get() == NULL) |
347 { | |
348 LOG(ERROR) << "Cannot convert to JSON file to a DICOM dataset: " << path; | |
349 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
350 } | |
351 | |
352 // VL Whole Slide Microscopy Image IOD | |
271
45e3b5adf4ae
opened issue 2379 in OpenSeadragon
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
265
diff
changeset
|
353 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SOPClassUID, OrthancWSI::VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE_IOD); |
0 | 354 |
355 // Slide Microscopy | |
356 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_Modality, "SM"); | |
357 | |
358 // Patient orientation makes no sense in whole-slide images | |
359 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_PatientOrientation, ""); | |
360 | |
361 // Some basic coordinate information | |
362 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_VolumetricProperties, "VOLUME"); | |
363 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ImageOrientationSlide, "0\\-1\\0\\-1\\0\\0"); | |
364 | |
365 std::string date, time; | |
130 | 366 Orthanc::SystemToolbox::GetNowDicom(date, time, true /* use UTC time (not local time) */); |
0 | 367 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyDate, date); |
368 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_StudyTime, time); | |
369 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesDate, date); | |
370 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_SeriesTime, time); | |
371 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentDate, date); | |
372 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_ContentTime, time); | |
373 OrthancWSI::DicomToolbox::SetStringTag(*dataset, DCM_AcquisitionDateTime, date + time); | |
374 | |
375 return dataset.release(); | |
376 } | |
377 | |
378 | |
379 | |
380 static void SetupDimension(DcmDataset& dataset, | |
381 const std::string& opticalPathId, | |
382 const OrthancWSI::ITiledPyramid& source, | |
383 const OrthancWSI::ImagedVolumeParameters& volume) | |
384 { | |
83 | 385 // Extract the identifier of the Dimension Organization, if provided |
386 std::string organization; | |
0 | 387 DcmItem* previous = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_DimensionOrganizationSequence); |
388 | |
83 | 389 if (previous != NULL && |
390 previous->tagExists(DCM_DimensionOrganizationUID)) | |
391 { | |
392 organization = OrthancWSI::DicomToolbox::GetStringTag(*previous, DCM_DimensionOrganizationUID); | |
393 } | |
394 else | |
0 | 395 { |
83 | 396 // No Dimension Organization provided: Generate an unique identifier |
397 organization = Orthanc::FromDcmtkBridge::GenerateUniqueIdentifier(Orthanc::ResourceType_Instance); | |
398 } | |
399 | |
400 | |
401 { | |
402 // 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
|
403 std::unique_ptr<DcmItem> item(new DcmItem); |
83 | 404 OrthancWSI::DicomToolbox::SetStringTag(*item, DCM_DimensionOrganizationUID, organization); |
405 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
406 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionOrganizationSequence)); |
83 | 407 |
408 if (!sequence->insert(item.release(), false, false).good() || | |
409 !dataset.insert(sequence.release(), true /* replace */, false).good()) | |
0 | 410 { |
83 | 411 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
0 | 412 } |
413 } | |
414 | |
83 | 415 |
0 | 416 { |
83 | 417 // 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
|
418 std::unique_ptr<DcmItem> item(new DcmItem); |
83 | 419 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
|
420 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
|
421 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
|
422 |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
423 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
|
424 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
|
425 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
|
426 OrthancWSI::DicomToolbox::SetAttributeTag(*item2, DCM_DimensionIndexPointer, DCM_RowPositionInTotalImagePixelMatrix); |
0 | 427 |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
428 std::unique_ptr<DcmSequenceOfItems> sequence(new DcmSequenceOfItems(DCM_DimensionIndexSequence)); |
0 | 429 |
83 | 430 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
|
431 !sequence->insert(item2.release(), false, false).good() || |
83 | 432 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
433 { | |
434 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
435 } | |
0 | 436 } |
437 | |
438 | |
83 | 439 { |
440 // 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
|
441 std::unique_ptr<DcmItem> item(new DcmItem); |
168
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
442 |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
443 std::unique_ptr<DcmItem> item3(new DcmItem); |
168
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
444 OrthancWSI::DicomToolbox::SetStringTag(*item3, DCM_OpticalPathIdentifier, opticalPathId); |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
445 |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
446 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
|
447 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
|
448 |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
449 if (!sequence3->insert(item3.release(), false, false).good() || |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
450 !item->insert(sequence3.release(), false, false).good() || |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
451 !sequence->insert(item.release(), false, false).good() || |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
452 !dataset.insert(sequence.release(), true /* replace */, false).good()) |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
453 { |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
454 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); |
d3aea0af03e1
attempt to fix issue 139
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
167
diff
changeset
|
455 } |
0 | 456 } |
457 } | |
458 | |
459 | |
460 static void EnrichDataset(DcmDataset& dataset, | |
461 const OrthancWSI::ITiledPyramid& source, | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
462 OrthancWSI::ImageCompression sourceCompression, |
0 | 463 const OrthancWSI::DicomizerParameters& parameters, |
464 const OrthancWSI::ImagedVolumeParameters& volume) | |
465 { | |
466 Orthanc::Encoding encoding = Orthanc::FromDcmtkBridge::DetectEncoding(dataset, Orthanc::Encoding_Latin1); | |
467 | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
468 if (sourceCompression == OrthancWSI::ImageCompression_Jpeg || |
0 | 469 parameters.GetTargetCompression() == OrthancWSI::ImageCompression_Jpeg) |
470 { | |
471 // Takes as estimation a 1:10 compression ratio | |
472 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "01"); | |
473 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionRatio, "10"); | |
474 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompressionMethod, "ISO_10918_1"); // JPEG Lossy Compression | |
475 } | |
476 else | |
477 { | |
478 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_LossyImageCompression, "00"); | |
479 } | |
480 | |
481 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeWidth, boost::lexical_cast<std::string>(volume.GetWidth())); | |
482 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeHeight, boost::lexical_cast<std::string>(volume.GetHeight())); | |
483 OrthancWSI::DicomToolbox::SetStringTag(dataset, DCM_ImagedVolumeDepth, boost::lexical_cast<std::string>(volume.GetDepth())); | |
484 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
485 std::unique_ptr<DcmItem> origin(new DcmItem); |
0 | 486 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_XOffsetInSlideCoordinateSystem, |
487 boost::lexical_cast<std::string>(volume.GetOffsetX())); | |
488 OrthancWSI::DicomToolbox::SetStringTag(*origin, DCM_YOffsetInSlideCoordinateSystem, | |
489 boost::lexical_cast<std::string>(volume.GetOffsetY())); | |
490 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
491 std::unique_ptr<DcmSequenceOfItems> sequenceOrigin(new DcmSequenceOfItems(DCM_TotalPixelMatrixOriginSequence)); |
0 | 492 if (!sequenceOrigin->insert(origin.release(), false, false).good() || |
493 !dataset.insert(sequenceOrigin.release(), false, false).good()) | |
494 { | |
495 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
496 } | |
497 | |
498 | |
499 if (parameters.GetOpticalPath() == OrthancWSI::OpticalPath_Brightfield) | |
500 { | |
501 if (dataset.tagExists(DCM_OpticalPathSequence)) | |
502 { | |
503 LOG(ERROR) << "The user DICOM dataset already contains an optical path sequence, giving up"; | |
504 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
505 } | |
506 | |
507 std::string brightfield; | |
508 Orthanc::EmbeddedResources::GetFileResource(brightfield, Orthanc::EmbeddedResources::BRIGHTFIELD_OPTICAL_PATH); | |
509 | |
510 Json::Value json; | |
226 | 511 if (!ReadJsonWithoutComments(json, brightfield)) |
0 | 512 { |
513 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
514 } | |
515 | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
516 std::unique_ptr<DcmElement> element(Orthanc::FromDcmtkBridge::FromJson( |
0 | 517 Orthanc::DicomTag(DCM_OpticalPathSequence.getGroup(), |
518 DCM_OpticalPathSequence.getElement()), | |
177
ea62c89b264b
fix due to change in the orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
175
diff
changeset
|
519 json, false, encoding, |
ea62c89b264b
fix due to change in the orthanc framework
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
175
diff
changeset
|
520 "" /* no private tag, thus no private creator */)); |
0 | 521 if (!dataset.insert(element.release()).good()) |
522 { | |
523 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
524 } | |
525 } | |
526 | |
527 | |
528 std::string profile; | |
529 if (parameters.GetIccProfilePath().empty()) | |
530 { | |
531 Orthanc::EmbeddedResources::GetFileResource(profile, Orthanc::EmbeddedResources::SRGB_ICC_PROFILE); | |
532 } | |
533 else | |
534 { | |
43 | 535 Orthanc::SystemToolbox::ReadFile(profile, parameters.GetIccProfilePath()); |
0 | 536 } |
537 | |
538 | |
539 DcmItem* opticalPath = OrthancWSI::DicomToolbox::ExtractSingleSequenceItem(dataset, DCM_OpticalPathSequence); | |
540 if (opticalPath == NULL) | |
541 { | |
542 LOG(ERROR) << "No optical path specified"; | |
543 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
544 } | |
545 | |
546 if (!opticalPath->tagExists(DCM_ICCProfile)) | |
547 { | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
548 std::unique_ptr<DcmOtherByteOtherWord> icc(new DcmOtherByteOtherWord(DCM_ICCProfile)); |
0 | 549 |
550 if (!icc->putUint8Array(reinterpret_cast<const Uint8*>(profile.c_str()), profile.size()).good() || | |
551 !opticalPath->insert(icc.release()).good()) | |
552 { | |
553 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
554 } | |
555 } | |
556 | |
557 const char* opticalPathId = NULL; | |
558 if (!opticalPath->findAndGetString(DCM_OpticalPathIdentifier, opticalPathId).good() || | |
559 opticalPathId == NULL) | |
560 { | |
561 LOG(ERROR) << "No identifier in the optical path"; | |
562 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
563 } | |
564 | |
565 SetupDimension(dataset, opticalPathId, source, volume); | |
566 } | |
567 | |
568 | |
569 static bool ParseParameters(int& exitStatus, | |
570 OrthancWSI::DicomizerParameters& parameters, | |
571 OrthancWSI::ImagedVolumeParameters& volume, | |
572 int argc, | |
573 char* argv[]) | |
574 { | |
575 // Declare the supported parameters | |
576 boost::program_options::options_description generic("Generic options"); | |
577 generic.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
578 (OPTION_HELP, "Display this help and exit") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
579 (OPTION_VERSION, "Output version information and exit") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
580 (OPTION_VERBOSE, "Be verbose in logs") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
581 (OPTION_THREADS, |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
582 boost::program_options::value<int>()->default_value(parameters.GetThreadsCount()), |
0 | 583 "Number of processing threads to be used") |
324
a92bb720f90b
renamed option --tiff-alignment as --padding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
323
diff
changeset
|
584 (OPTION_FORCE_OPENSLIDE, boost::program_options::value<bool>()->default_value(false), |
323
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
585 "Whether to force the use of OpenSlide on input TIFF-like files (Boolean)") |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
586 (OPTION_OPENSLIDE, boost::program_options::value<std::string>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
587 "Path to the shared library of OpenSlide " |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
588 "(not necessary if converting from standard hierarchical TIFF)") |
0 | 589 ; |
590 | |
591 boost::program_options::options_description source("Options for the source image"); | |
592 source.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
593 (OPTION_DATASET, boost::program_options::value<std::string>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
594 "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
|
595 (OPTION_SAMPLE_DATASET, |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
596 "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
|
597 (OPTION_REENCODE, boost::program_options::value<bool>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
598 "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
|
599 (OPTION_REPAINT, boost::program_options::value<bool>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
600 "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
|
601 (OPTION_COLOR, boost::program_options::value<std::string>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
602 "Color of the background (e.g. \"255,0,0\")") |
324
a92bb720f90b
renamed option --tiff-alignment as --padding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
323
diff
changeset
|
603 (OPTION_PADDING, boost::program_options::value<int>()->default_value(1), |
a92bb720f90b
renamed option --tiff-alignment as --padding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
323
diff
changeset
|
604 "Add padding to plain PNG/JPEG/TIFF images to align the width/height to multiples " |
a92bb720f90b
renamed option --tiff-alignment as --padding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
323
diff
changeset
|
605 "of this value, which enables deep zoom with IIIF (1 means no padding)") |
0 | 606 ; |
607 | |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
608 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
|
609 cytomine.add_options() |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
610 (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
|
611 "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
|
612 (OPTION_CYTOMINE_PUBLIC_KEY, boost::program_options::value<std::string>(), |
246 | 613 "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
|
614 (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
|
615 "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
|
616 (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
|
617 "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
|
618 (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
|
619 "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
|
620 "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
|
621 ; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
622 |
0 | 623 boost::program_options::options_description pyramid("Options to construct the pyramid"); |
624 pyramid.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
625 (OPTION_PYRAMID, boost::program_options::value<bool>()->default_value(false), |
0 | 626 "Reconstruct the full pyramid (slow) (Boolean)") |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
627 (OPTION_SMOOTH, boost::program_options::value<bool>()->default_value(false), |
0 | 628 "Apply smoothing when reconstructing the pyramid " |
629 "(slower, but higher quality) (Boolean)") | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
630 (OPTION_LEVELS, boost::program_options::value<int>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
631 "Number of levels in the target pyramid") |
0 | 632 ; |
633 | |
634 boost::program_options::options_description target("Options for the target image"); | |
635 target.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
636 (OPTION_TILE_WIDTH, boost::program_options::value<int>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
637 "Width of the tiles in the target image") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
638 (OPTION_TILE_HEIGHT, boost::program_options::value<int>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
639 "Height of the tiles in the target image") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
640 (OPTION_COMPRESSION, boost::program_options::value<std::string>(), |
0 | 641 "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
|
642 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
643 "Set quality level for JPEG (0..100)") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
644 (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
|
645 "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
|
646 (OPTION_FOLDER, boost::program_options::value<std::string>(), |
0 | 647 "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
|
648 (OPTION_FOLDER_PATTERN, |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
649 boost::program_options::value<std::string>()->default_value("wsi-%06d.dcm"), |
0 | 650 "Pattern for the files in the output folder") |
651 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"), | |
652 "URL to the REST API of the target Orthanc server") | |
653 ; | |
654 | |
655 boost::program_options::options_description volumeOptions("Description of the imaged volume"); | |
656 volumeOptions.add_options() | |
279
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
657 (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
|
658 "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
|
659 (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
|
660 "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
|
661 (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
|
662 "Depth of the specimen (in mm)") |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
663 (OPTION_OFFSET_X, boost::program_options::value<float>()->default_value(20), |
0 | 664 "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
|
665 (OPTION_OFFSET_Y, boost::program_options::value<float>()->default_value(40), |
0 | 666 "Y offset the specimen, wrt. slide coordinates origin (in mm)") |
667 ; | |
668 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
669 boost::program_options::options_description restOptions |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
670 ("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
|
671 OrthancWSI::ApplicationToolbox::AddRestApiOptions(restOptions); |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
672 |
0 | 673 boost::program_options::options_description advancedOptions("Advanced options"); |
674 advancedOptions.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
675 (OPTION_OPTICAL_PATH, boost::program_options::value<std::string>()->default_value("brightfield"), |
0 | 676 "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
|
677 (OPTION_ICC_PROFILE, boost::program_options::value<std::string>(), |
0 | 678 "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
|
679 (OPTION_SAFETY, boost::program_options::value<bool>()->default_value(true), |
0 | 680 "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
|
681 (OPTION_LOWER_LEVELS, boost::program_options::value<int>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
682 "Number of pyramid levels up to which multithreading " |
0 | 683 "should be applied (only for performance/memory tuning)") |
684 ; | |
685 | |
686 boost::program_options::options_description hidden; | |
687 hidden.add_options() | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
688 (OPTION_INPUT, boost::program_options::value<std::string>(), |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
689 "Input file"); |
0 | 690 ; |
691 | |
692 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
|
693 allWithoutHidden |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
694 .add(generic) |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
695 .add(source) |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
696 .add(cytomine) |
125
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
697 .add(pyramid) |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
698 .add(target) |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
699 .add(volumeOptions) |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
700 .add(restOptions) |
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
701 .add(advancedOptions); |
0 | 702 |
703 boost::program_options::options_description all = allWithoutHidden; | |
704 all.add(hidden); | |
705 | |
706 boost::program_options::positional_options_description positional; | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
707 positional.add(OPTION_INPUT, 1); |
0 | 708 |
709 boost::program_options::variables_map options; | |
710 bool error = false; | |
711 | |
712 try | |
713 { | |
714 boost::program_options::store(boost::program_options::command_line_parser(argc, argv). | |
715 options(all).positional(positional).run(), options); | |
716 boost::program_options::notify(options); | |
717 } | |
718 catch (boost::program_options::error& e) | |
719 { | |
720 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what(); | |
721 error = true; | |
722 } | |
723 | |
724 if (!error && | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
725 options.count(OPTION_SAMPLE_DATASET)) |
0 | 726 { |
727 std::string sample; | |
728 Orthanc::EmbeddedResources::GetFileResource(sample, Orthanc::EmbeddedResources::SAMPLE_DATASET); | |
729 | |
730 std::cout << std::endl << sample << std::endl; | |
731 | |
732 return false; | |
733 } | |
734 | |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
735 // New in release 1.1 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
736 if (options.count(OPTION_CYTOMINE_URL) || |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
737 options.count(OPTION_CYTOMINE_PUBLIC_KEY) || |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
738 options.count(OPTION_CYTOMINE_PRIVATE_KEY) || |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
739 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
|
740 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
741 if (!options.count(OPTION_CYTOMINE_URL)) |
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
744 "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
|
745 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
746 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
747 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
|
748 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
749 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
750 "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
|
751 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
752 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
753 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
|
754 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
755 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
756 "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
|
757 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
758 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
759 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
|
760 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
761 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
762 "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
|
763 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
764 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
765 if (!options.count(OPTION_CYTOMINE_COMPRESSION)) |
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
768 "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
|
769 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
770 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
771 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
|
772 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
773 OrthancWSI::ImageCompression compression; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
774 if (s == "jpeg") |
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_Jpeg; |
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 if (s == "png") |
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 compression = OrthancWSI::ImageCompression_Png; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
781 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
782 else |
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
785 "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
|
786 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
787 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
788 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
|
789 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
|
790 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
|
791 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
|
792 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
793 |
0 | 794 if (!error && |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
795 options.count(OPTION_HELP) == 0 && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
796 options.count(OPTION_VERSION) == 0 && |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
797 options.count(OPTION_INPUT) != 1 && |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
798 !parameters.IsCytomineSource()) |
0 | 799 { |
800 LOG(ERROR) << "No input file was specified"; | |
801 error = true; | |
802 } | |
803 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
804 if (error || options.count(OPTION_HELP)) |
0 | 805 { |
806 std::cout << std::endl | |
807 << "Usage: " << argv[0] << " [OPTION]... [INPUT]" | |
808 << std::endl | |
809 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research." | |
810 << std::endl << std::endl | |
811 << "Create a DICOM file from a digital pathology image." | |
812 << std::endl; | |
813 | |
814 std::cout << allWithoutHidden << "\n"; | |
815 | |
816 if (error) | |
817 { | |
818 exitStatus = -1; | |
819 } | |
820 | |
821 return false; | |
822 } | |
823 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
824 if (options.count(OPTION_VERSION)) |
8
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
825 { |
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
826 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]); |
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
827 return false; |
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
828 } |
62adabb8c122
Provide "--version" in command-line tools
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
0
diff
changeset
|
829 |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
830 if (options.count(OPTION_VERBOSE)) |
0 | 831 { |
832 Orthanc::Logging::EnableInfoLevel(true); | |
833 } | |
834 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
835 if (options.count(OPTION_OPENSLIDE)) |
0 | 836 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
837 OrthancWSI::OpenSlideLibrary::Initialize(options[OPTION_OPENSLIDE].as<std::string>()); |
0 | 838 } |
839 | |
323
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
840 if (options.count(OPTION_FORCE_OPENSLIDE) && |
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
841 options[OPTION_FORCE_OPENSLIDE].as<bool>()) |
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
842 { |
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
843 parameters.SetForceOpenSlide(true); |
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
844 } |
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
845 |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
846 if (options.count(OPTION_PYRAMID) && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
847 options[OPTION_PYRAMID].as<bool>()) |
0 | 848 { |
849 parameters.SetReconstructPyramid(true); | |
850 } | |
851 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
852 if (options.count(OPTION_SMOOTH) && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
853 options[OPTION_SMOOTH].as<bool>()) |
0 | 854 { |
855 parameters.SetSmoothEnabled(true); | |
856 } | |
857 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
858 if (options.count(OPTION_SAFETY) && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
859 options[OPTION_SAFETY].as<bool>()) |
0 | 860 { |
861 parameters.SetSafetyCheck(true); | |
862 } | |
863 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
864 if (options.count(OPTION_REENCODE) && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
865 options[OPTION_REENCODE].as<bool>()) |
0 | 866 { |
867 parameters.SetForceReencode(true); | |
868 } | |
869 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
870 if (options.count(OPTION_REPAINT) && |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
871 options[OPTION_REPAINT].as<bool>()) |
0 | 872 { |
873 parameters.SetRepaintBackground(true); | |
874 } | |
875 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
876 if (options.count(OPTION_TILE_WIDTH) || |
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
877 options.count(OPTION_TILE_HEIGHT)) |
0 | 878 { |
879 int w = 0; | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
880 if (options.count(OPTION_TILE_WIDTH)) |
0 | 881 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
882 w = options[OPTION_TILE_WIDTH].as<int>(); |
0 | 883 } |
884 | |
145 | 885 int h = 0; |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
886 if (options.count(OPTION_TILE_HEIGHT)) |
0 | 887 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
888 h = options[OPTION_TILE_HEIGHT].as<int>(); |
0 | 889 } |
890 | |
891 if (w < 0 || h < 0) | |
892 { | |
893 LOG(ERROR) << "Negative target tile size specified: " << w << "x" << h; | |
894 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
895 } | |
896 | |
897 parameters.SetTargetTileSize(w, h); | |
898 } | |
899 | |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
900 if (!parameters.IsCytomineSource()) |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
901 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
902 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
|
903 } |
0 | 904 |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
905 if (options.count(OPTION_COLOR)) |
0 | 906 { |
907 uint8_t r, g, b; | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
908 OrthancWSI::ApplicationToolbox::ParseColor(r, g, b, options[OPTION_COLOR].as<std::string>()); |
0 | 909 parameters.SetBackgroundColor(r, g, b); |
910 } | |
911 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
912 if (options.count(OPTION_COMPRESSION)) |
0 | 913 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
914 std::string s = options[OPTION_COMPRESSION].as<std::string>(); |
0 | 915 if (s == "none") |
916 { | |
917 parameters.SetTargetCompression(OrthancWSI::ImageCompression_None); | |
918 } | |
919 else if (s == "jpeg") | |
920 { | |
921 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg); | |
922 } | |
923 else if (s == "jpeg2000") | |
924 { | |
925 parameters.SetTargetCompression(OrthancWSI::ImageCompression_Jpeg2000); | |
926 } | |
927 else | |
928 { | |
929 LOG(ERROR) << "Unknown image compression for the target image: " << s; | |
930 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
931 } | |
932 } | |
933 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
934 if (options.count(OPTION_JPEG_QUALITY)) |
0 | 935 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
936 parameters.SetJpegQuality(options[OPTION_JPEG_QUALITY].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_LEVELS)) |
0 | 940 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
941 parameters.SetPyramidLevelsCount(options[OPTION_LEVELS].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_LOWER_LEVELS)) |
0 | 945 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
946 parameters.SetPyramidLowerLevelsCount(options[OPTION_LOWER_LEVELS].as<int>()); |
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_THREADS)) |
0 | 950 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
951 parameters.SetThreadsCount(options[OPTION_THREADS].as<int>()); |
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_MAX_SIZE)) |
0 | 955 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
956 parameters.SetDicomMaxFileSize(options[OPTION_MAX_SIZE].as<int>() * 1024 * 1024); |
0 | 957 } |
958 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
959 if (options.count(OPTION_FOLDER)) |
0 | 960 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
961 parameters.SetTargetFolder(options[OPTION_FOLDER].as<std::string>()); |
0 | 962 } |
963 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
964 if (options.count(OPTION_FOLDER_PATTERN)) |
0 | 965 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
966 parameters.SetTargetFolderPattern(options[OPTION_FOLDER_PATTERN].as<std::string>()); |
0 | 967 } |
968 | |
125
7a3f4d580625
SSL is enabled by default for HTTPS transfers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
123
diff
changeset
|
969 OrthancWSI::ApplicationToolbox::SetupRestApi(parameters.GetOrthancParameters(), options); |
0 | 970 |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
971 if (options.count(OPTION_DATASET)) |
0 | 972 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
973 parameters.SetDatasetPath(options[OPTION_DATASET].as<std::string>()); |
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_WIDTH)) |
0 | 977 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
978 volume.SetWidth(options[OPTION_IMAGED_WIDTH].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_IMAGED_HEIGHT)) |
0 | 982 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
983 volume.SetHeight(options[OPTION_IMAGED_HEIGHT].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_IMAGED_DEPTH)) |
0 | 987 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
988 volume.SetDepth(options[OPTION_IMAGED_DEPTH].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_OFFSET_X)) |
0 | 992 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
993 volume.SetOffsetX(options[OPTION_OFFSET_X].as<float>()); |
0 | 994 } |
995 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
996 if (options.count(OPTION_OFFSET_Y)) |
0 | 997 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
998 volume.SetOffsetY(options[OPTION_OFFSET_Y].as<float>()); |
0 | 999 } |
1000 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
1001 if (options.count(OPTION_OPTICAL_PATH)) |
0 | 1002 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
1003 std::string s = options[OPTION_OPTICAL_PATH].as<std::string>(); |
0 | 1004 if (s == "none") |
1005 { | |
1006 parameters.SetOpticalPath(OrthancWSI::OpticalPath_None); | |
1007 } | |
1008 else if (s == "brightfield") | |
1009 { | |
1010 parameters.SetOpticalPath(OrthancWSI::OpticalPath_Brightfield); | |
1011 } | |
1012 else | |
1013 { | |
1014 LOG(ERROR) << "Unknown optical path definition: " << s; | |
1015 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
1016 } | |
1017 } | |
1018 | |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
1019 if (options.count(OPTION_ICC_PROFILE)) |
0 | 1020 { |
129
806d1bb56918
cleaning up options in Dicomizer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
1021 parameters.SetIccProfilePath(options[OPTION_ICC_PROFILE].as<std::string>()); |
0 | 1022 } |
1023 | |
324
a92bb720f90b
renamed option --tiff-alignment as --padding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
323
diff
changeset
|
1024 if (options.count(OPTION_PADDING)) |
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
|
1025 { |
324
a92bb720f90b
renamed option --tiff-alignment as --padding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
323
diff
changeset
|
1026 int value = options[OPTION_PADDING].as<int>(); |
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
|
1027 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
|
1028 { |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1029 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange, |
324
a92bb720f90b
renamed option --tiff-alignment as --padding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
323
diff
changeset
|
1030 "Padding must be >= 1"); |
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
|
1031 } |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1032 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
|
1033 { |
324
a92bb720f90b
renamed option --tiff-alignment as --padding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
323
diff
changeset
|
1034 parameters.SetPadding(static_cast<unsigned int>(value)); |
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
|
1035 } |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1036 } |
fa734a851551
New option: "tiff-alignment" to control deep zoom of plain TIFF over IIIF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
289
diff
changeset
|
1037 |
0 | 1038 return true; |
1039 } | |
1040 | |
1041 | |
167
605247fc8758
Fix issue #144 (OrthancWSIDicomizer PhotometricInterpretation)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
166
diff
changeset
|
1042 |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1043 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
|
1044 OrthancWSI::ImagedVolumeParameters& volume, |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1045 const std::string& path, |
0 | 1046 const OrthancWSI::DicomizerParameters& parameters) |
1047 { | |
244
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1048 if (parameters.IsCytomineSource()) |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1049 { |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1050 // New in release 1.1 |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1051 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
|
1052 << " from Cytomine server: " << parameters.GetCytomineServer().GetUrl(); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1053 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1054 return new OrthancWSI::CytomineImage(parameters.GetCytomineServer(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1055 parameters.GetCytominePublicKey(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1056 parameters.GetCytominePrivateKey(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1057 parameters.GetCytomineImageInstanceId(), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1058 parameters.GetTargetTileWidth(512), |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1059 parameters.GetTargetTileHeight(512)); |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1060 } |
4273518c2009
OrthancWSIDicomizer: Support importing of images from Cytomine
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
242
diff
changeset
|
1061 |
0 | 1062 LOG(WARNING) << "The input image is: " << path; |
1063 | |
1064 OrthancWSI::ImageCompression format = OrthancWSI::DetectFormatFromFile(path); | |
1065 LOG(WARNING) << "File format of the input image: " << EnumerationToString(format); | |
1066 | |
1067 switch (format) | |
1068 { | |
1069 case OrthancWSI::ImageCompression_Png: | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1070 { |
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1071 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 1072 return new OrthancWSI::TiledPngImage(path, |
1073 parameters.GetTargetTileWidth(512), | |
1074 parameters.GetTargetTileHeight(512)); | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1075 } |
0 | 1076 |
1077 case OrthancWSI::ImageCompression_Jpeg: | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1078 { |
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1079 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
0 | 1080 return new OrthancWSI::TiledJpegImage(path, |
1081 parameters.GetTargetTileWidth(512), | |
1082 parameters.GetTargetTileHeight(512)); | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1083 } |
0 | 1084 |
1085 case OrthancWSI::ImageCompression_Tiff: | |
1086 { | |
323
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
1087 if (parameters.IsForceOpenSlide()) |
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
1088 { |
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
1089 LOG(WARNING) << "Forcing the use of OpenSlide on a TIFF-like file"; |
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
1090 break; |
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
1091 } |
429c4efa1fde
added option --force-openslide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
322
diff
changeset
|
1092 |
0 | 1093 try |
1094 { | |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
1095 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
|
1096 sourceCompression = tiff->GetImageCompression(); |
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1097 return tiff.release(); |
0 | 1098 } |
1099 catch (Orthanc::OrthancException&) | |
1100 { | |
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
|
1101 LOG(WARNING) << "This is not a standard hierarchical TIFF file, fallback to plain TIFF"; |
0 | 1102 } |
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
|
1103 |
322
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1104 try |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1105 { |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1106 sourceCompression = OrthancWSI::ImageCompression_Unknown; |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1107 return new OrthancWSI::PlainTiff(path, |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1108 parameters.GetTargetTileWidth(512), |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1109 parameters.GetTargetTileHeight(512), |
324
a92bb720f90b
renamed option --tiff-alignment as --padding
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
323
diff
changeset
|
1110 parameters.GetPadding(), |
322
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1111 parameters.GetBackgroundColorRed(), |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1112 parameters.GetBackgroundColorGreen(), |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1113 parameters.GetBackgroundColorBlue()); |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1114 } |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1115 catch (Orthanc::OrthancException&) |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1116 { |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1117 LOG(WARNING) << "This is not a standard plain TIFF file, fallback to OpenSlide (if enabled)"; |
778e08291d52
re-enabling built-in support of plain TIFF
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
319
diff
changeset
|
1118 } |
0 | 1119 } |
1120 | |
1121 default: | |
1122 break; | |
1123 } | |
1124 | |
1125 try | |
1126 { | |
1127 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
|
1128 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
|
1129 |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1130 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
|
1131 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
|
1132 parameters.GetTargetTileHeight(512))); |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1133 |
315
072968f00d26
support of transparency in OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
312
diff
changeset
|
1134 openslide->SetBackgroundColor(parameters.GetBackgroundColorRed(), |
072968f00d26
support of transparency in OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
312
diff
changeset
|
1135 parameters.GetBackgroundColorGreen(), |
072968f00d26
support of transparency in OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
312
diff
changeset
|
1136 parameters.GetBackgroundColorBlue()); |
072968f00d26
support of transparency in OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
312
diff
changeset
|
1137 |
279
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1138 float volumeWidth, volumeHeight; |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1139 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
|
1140 { |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1141 if (!volume.HasWidth()) |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1142 { |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1143 volume.SetWidth(volumeWidth); |
281 | 1144 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
|
1145 } |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1146 |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1147 if (!volume.HasHeight()) |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1148 { |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1149 volume.SetHeight(volumeHeight); |
281 | 1150 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
|
1151 } |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1152 } |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1153 |
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1154 return openslide.release(); |
0 | 1155 } |
1156 catch (Orthanc::OrthancException&) | |
1157 { | |
1158 LOG(ERROR) << "This file is not supported by OpenSlide"; | |
1159 return NULL; | |
1160 } | |
1161 } | |
1162 | |
1163 | |
1164 int main(int argc, char* argv[]) | |
1165 { | |
1166 OrthancWSI::ApplicationToolbox::GlobalInitialize(); | |
93
14146ecd1688
Display version of the framework in the logs
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
84
diff
changeset
|
1167 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]); |
0 | 1168 |
1169 int exitStatus = 0; | |
1170 | |
1171 try | |
1172 { | |
1173 OrthancWSI::DicomizerParameters parameters; | |
1174 OrthancWSI::ImagedVolumeParameters volume; | |
1175 | |
1176 if (ParseParameters(exitStatus, parameters, volume, argc, argv)) | |
1177 { | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1178 OrthancWSI::ImageCompression sourceCompression; |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
1179 std::unique_ptr<OrthancWSI::ITiledPyramid> source; |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1180 |
279
77afef2cf64b
automated extraction of the imaged volume if using OpenSlide
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
254
diff
changeset
|
1181 source.reset(OpenInputPyramid(sourceCompression, volume, parameters.GetInputFile(), parameters)); |
0 | 1182 if (source.get() == NULL) |
1183 { | |
1184 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
1185 } | |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1186 |
289
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1187 // 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
|
1188 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
|
1189 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
|
1190 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
|
1191 { |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1192 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
|
1193 << "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
|
1194 << OPTION_IMAGED_HEIGHT << " options: " << pixelSpacingX << " vs. " << pixelSpacingY; |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1195 } |
5f783bf882fe
add warning about anisotropic pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
282
diff
changeset
|
1196 |
57
91fc9583b2de
big refactoring to support sparse tiling
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
43
diff
changeset
|
1197 LOG(WARNING) << "Compression of the individual source tiles: " << OrthancWSI::EnumerationToString(sourceCompression); |
0 | 1198 |
1199 // 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
|
1200 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
|
1201 EnrichDataset(*dataset, *source, sourceCompression, parameters, volume); |
0 | 1202 |
199
a1c265cb2174
replacing deprecated std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
1203 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
|
1204 Recompress(*output, *source, *dataset, parameters, volume, sourceCompression); |
0 | 1205 } |
1206 } | |
1207 catch (Orthanc::OrthancException& e) | |
1208 { | |
1209 LOG(ERROR) << "Terminating on exception: " << e.What(); | |
1210 exitStatus = -1; | |
1211 } | |
1212 | |
1213 OrthancWSI::ApplicationToolbox::GlobalFinalize(); | |
1214 | |
1215 return exitStatus; | |
1216 } |