Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1677:51bab5188a13
start multiple preset windowings
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Mon, 23 Nov 2020 19:24:18 +0100 |
parents | 4e14735e98f8 |
children | 5b8b88e5bfd6 |
rev | line source |
---|---|
746 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
1270
2d8ab34c8c91
upgrade to year 2020
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1206
diff
changeset
|
5 * Copyright (C) 2017-2020 Osimis S.A., Belgium |
746 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
1598
8563ea5d8ae4
relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1596
diff
changeset
|
8 * modify it under the terms of the GNU Lesser General Public License |
746 | 9 * as published by the Free Software Foundation, either version 3 of |
10 * the License, or (at your option) any later version. | |
11 * | |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
1598
8563ea5d8ae4
relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1596
diff
changeset
|
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
8563ea5d8ae4
relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1596
diff
changeset
|
15 * Lesser General Public License for more details. |
1596
4fb8fdf03314
removed annoying whitespace
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1571
diff
changeset
|
16 * |
1598
8563ea5d8ae4
relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1596
diff
changeset
|
17 * You should have received a copy of the GNU Lesser General Public |
8563ea5d8ae4
relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1596
diff
changeset
|
18 * License along with this program. If not, see |
8563ea5d8ae4
relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1596
diff
changeset
|
19 * <http://www.gnu.org/licenses/>. |
746 | 20 **/ |
21 | |
22 | |
23 #include "DicomInstanceParameters.h" | |
24 | |
25 #include "../Scene2D/ColorTextureSceneLayer.h" | |
26 #include "../Scene2D/FloatTextureSceneLayer.h" | |
27 #include "../Toolbox/GeometryToolbox.h" | |
1287
8e82fdc6200e
Heavy (temporary) logging in the path that leads
Benjamin Golinvaux <bgo@osimis.io>
parents:
1270
diff
changeset
|
28 #include "../Toolbox/ImageToolbox.h" |
746 | 29 |
1455
30deba7bc8e2
simplifying include_directories
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1353
diff
changeset
|
30 #include <Images/Image.h> |
30deba7bc8e2
simplifying include_directories
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1353
diff
changeset
|
31 #include <Images/ImageProcessing.h> |
30deba7bc8e2
simplifying include_directories
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1353
diff
changeset
|
32 #include <Logging.h> |
30deba7bc8e2
simplifying include_directories
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1353
diff
changeset
|
33 #include <OrthancException.h> |
30deba7bc8e2
simplifying include_directories
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1353
diff
changeset
|
34 #include <Toolbox.h> |
746 | 35 |
36 | |
37 namespace OrthancStone | |
38 { | |
1636 | 39 static void ExtractFrameOffsets(Vector& target, |
40 const Orthanc::DicomMap& dicom, | |
41 unsigned int numberOfFrames) | |
746 | 42 { |
43 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html | |
44 | |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
45 std::string increment; |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
46 |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
47 if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false)) |
746 | 48 { |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
49 Orthanc::Toolbox::ToUpperCase(increment); |
1635
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
50 |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
51 // This is the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
52 if (increment != "3004,000C") |
746 | 53 { |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
54 LOG(WARNING) << "Bad value for the FrameIncrementPointer tags in a multiframe image"; |
1636 | 55 target.resize(0); |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
56 return; |
746 | 57 } |
58 } | |
59 | |
1636 | 60 if (!LinearAlgebra::ParseVector(target, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) || |
61 target.size() != numberOfFrames) | |
746 | 62 { |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
63 LOG(INFO) << "The frame offset information is missing in a multiframe image"; |
1635
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
64 |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
65 // DO NOT use ".clear()" here, as the "Vector" class doesn't behave like std::vector! |
1636 | 66 target.resize(0); |
746 | 67 } |
68 } | |
69 | |
70 | |
1642
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
71 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom) |
746 | 72 { |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
980
diff
changeset
|
73 if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) || |
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
980
diff
changeset
|
74 !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) || |
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
980
diff
changeset
|
75 !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) |
746 | 76 { |
77 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
78 } | |
79 | |
80 std::string s; | |
1635
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
81 if (dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) |
746 | 82 { |
1635
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
83 sopClassUid_ = StringToSopClassUid(s); |
746 | 84 } |
85 else | |
86 { | |
1635
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
87 sopClassUid_ = SopClassUid_Other; |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
88 } |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
89 |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
90 uint32_t n; |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
91 if (dicom.ParseUnsignedInteger32(n, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES)) |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
92 { |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
93 numberOfFrames_ = n; |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
94 } |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
95 else |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
96 { |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
97 numberOfFrames_ = 1; |
746 | 98 } |
99 | |
1635
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
100 if (!dicom.HasTag(Orthanc::DICOM_TAG_COLUMNS) || |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
101 !dicom.GetValue(Orthanc::DICOM_TAG_COLUMNS).ParseFirstUnsignedInteger(width_)) |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
102 { |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
103 width_ = 0; |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
104 } |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
105 |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
106 if (!dicom.HasTag(Orthanc::DICOM_TAG_ROWS) || |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
107 !dicom.GetValue(Orthanc::DICOM_TAG_ROWS).ParseFirstUnsignedInteger(height_)) |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
108 { |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
109 height_ = 0; |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
110 } |
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
111 |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
112 if (!dicom.ParseDouble(sliceThickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS)) |
746 | 113 { |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
114 sliceThickness_ = 100.0 * std::numeric_limits<double>::epsilon(); |
746 | 115 } |
116 | |
117 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom); | |
118 | |
119 std::string position, orientation; | |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
980
diff
changeset
|
120 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) && |
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
980
diff
changeset
|
121 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false)) |
746 | 122 { |
123 geometry_ = CoordinateSystem3D(position, orientation); | |
124 } | |
125 | |
1635
1a714e21ea7c
start refactoring DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1634
diff
changeset
|
126 // Must be AFTER setting "numberOfFrames_" |
1639 | 127 if (numberOfFrames_ > 1) |
128 { | |
129 ExtractFrameOffsets(frameOffsets_, dicom, numberOfFrames_); | |
130 } | |
131 else | |
132 { | |
133 frameOffsets_.resize(0); | |
134 } | |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
135 |
746 | 136 if (sopClassUid_ == SopClassUid_RTDose) |
137 { | |
1091
5a18e6a395bc
Added DoseUnit tag retrieval to DicomInstanceParameters
Benjamin Golinvaux <bgo@osimis.io>
parents:
1027
diff
changeset
|
138 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002); |
5a18e6a395bc
Added DoseUnit tag retrieval to DicomInstanceParameters
Benjamin Golinvaux <bgo@osimis.io>
parents:
1027
diff
changeset
|
139 |
5a18e6a395bc
Added DoseUnit tag retrieval to DicomInstanceParameters
Benjamin Golinvaux <bgo@osimis.io>
parents:
1027
diff
changeset
|
140 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false)) |
5a18e6a395bc
Added DoseUnit tag retrieval to DicomInstanceParameters
Benjamin Golinvaux <bgo@osimis.io>
parents:
1027
diff
changeset
|
141 { |
1141
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
142 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_; |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
143 doseUnits_.clear(); |
1091
5a18e6a395bc
Added DoseUnit tag retrieval to DicomInstanceParameters
Benjamin Golinvaux <bgo@osimis.io>
parents:
1027
diff
changeset
|
144 } |
746 | 145 } |
146 | |
147 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) && | |
148 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE)) | |
149 { | |
1141
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
150 if (sopClassUid_ == SopClassUid_RTDose) |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
151 { |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
152 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_; |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
153 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
154 hasRescale_ = false; |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
155 } |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
156 else |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
157 { |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
158 hasRescale_ = true; |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
159 } |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
160 |
746 | 161 } |
162 else | |
163 { | |
164 hasRescale_ = false; | |
165 } | |
166 | |
1141
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
167 if (dicom.ParseDouble(doseGridScaling_, Orthanc::DICOM_TAG_DOSE_GRID_SCALING)) |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
168 { |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
169 if (sopClassUid_ == SopClassUid_RTDose) |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
170 { |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
171 LOG(INFO) << "DOSE HAS DoseGridScaling: doseGridScaling_ = " << doseGridScaling_; |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
172 } |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
173 } |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
174 else |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
175 { |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
176 doseGridScaling_ = 1.0; |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
177 if (sopClassUid_ == SopClassUid_RTDose) |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
178 { |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
179 LOG(ERROR) << "Tag DoseGridScaling (0x3004, 0x000e) is missing in " << sopInstanceUid_ << " doseGridScaling_ will be set to 1.0"; |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
180 } |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
181 } |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
182 |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
183 bool ok = false; |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
184 |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
185 if (LinearAlgebra::ParseVector(presetWindowingCenters_, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) && |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
186 LinearAlgebra::ParseVector(presetWindowingWidths_, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH)) |
746 | 187 { |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
188 if (presetWindowingCenters_.size() == presetWindowingWidths_.size()) |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
189 { |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
190 ok = true; |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
191 } |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
192 else |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
193 { |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
194 LOG(ERROR) << "Mismatch in the number of preset windowing widths/centers, ignoring this"; |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
195 ok = false; |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
196 } |
746 | 197 } |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
198 |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
199 if (!ok) |
746 | 200 { |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
201 // Don't use "Vector::clear()", as it has not the same meaning as "std::vector::clear()" |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
202 presetWindowingCenters_.resize(0); |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
203 presetWindowingWidths_.resize(0); |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
204 } |
746 | 205 |
980
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
206 // This computes the "IndexInSeries" metadata from Orthanc (check |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
207 // out "Orthanc::ServerIndex::Store()") |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
208 hasIndexInSeries_ = ( |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
209 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) || |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
210 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX)); |
1646
4e14735e98f8
preparing to remove FrameExtent
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1642
diff
changeset
|
211 |
4e14735e98f8
preparing to remove FrameExtent
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1642
diff
changeset
|
212 if (!dicom.LookupStringValue( |
4e14735e98f8
preparing to remove FrameExtent
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1642
diff
changeset
|
213 frameOfReferenceUid_, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, false)) |
4e14735e98f8
preparing to remove FrameExtent
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1642
diff
changeset
|
214 { |
4e14735e98f8
preparing to remove FrameExtent
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1642
diff
changeset
|
215 frameOfReferenceUid_.clear(); |
4e14735e98f8
preparing to remove FrameExtent
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1642
diff
changeset
|
216 } |
746 | 217 } |
218 | |
219 | |
1642
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
220 const Orthanc::DicomImageInformation& DicomInstanceParameters::GetImageInformation() const |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
221 { |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
222 assert(tags_.get() != NULL); |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
223 |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
224 if (imageInformation_.get() == NULL) |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
225 { |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
226 const_cast<DicomInstanceParameters&>(*this).imageInformation_. |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
227 reset(new Orthanc::DicomImageInformation(GetTags())); |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
228 |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
229 assert(imageInformation_->GetWidth() == GetWidth()); |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
230 assert(imageInformation_->GetHeight() == GetHeight()); |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
231 assert(imageInformation_->GetNumberOfFrames() == GetNumberOfFrames()); |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
232 } |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
233 |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
234 assert(imageInformation_.get() != NULL); |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
235 return *imageInformation_; |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
236 } |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
237 |
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
238 |
1636 | 239 CoordinateSystem3D DicomInstanceParameters::GetFrameGeometry(unsigned int frame) const |
746 | 240 { |
1636 | 241 if (frame >= data_.numberOfFrames_) |
746 | 242 { |
243 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
244 } | |
1636 | 245 else if (data_.frameOffsets_.empty()) |
746 | 246 { |
1636 | 247 return data_.geometry_; |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
248 } |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
249 else |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
250 { |
1636 | 251 assert(data_.frameOffsets_.size() == data_.numberOfFrames_); |
746 | 252 |
253 return CoordinateSystem3D( | |
1636 | 254 data_.geometry_.GetOrigin() + data_.frameOffsets_[frame] * data_.geometry_.GetNormal(), |
255 data_.geometry_.GetAxisX(), | |
256 data_.geometry_.GetAxisY()); | |
746 | 257 } |
258 } | |
259 | |
260 | |
1636 | 261 bool DicomInstanceParameters::IsPlaneWithinSlice(unsigned int frame, |
262 const CoordinateSystem3D& plane) const | |
746 | 263 { |
1636 | 264 if (frame >= data_.numberOfFrames_) |
746 | 265 { |
266 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
267 } | |
268 | |
1636 | 269 CoordinateSystem3D tmp = data_.geometry_; |
746 | 270 |
271 if (frame != 0) | |
272 { | |
273 tmp = GetFrameGeometry(frame); | |
274 } | |
275 | |
276 double distance; | |
277 | |
757 | 278 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) && |
1636 | 279 distance <= data_.sliceThickness_ / 2.0); |
746 | 280 } |
281 | |
1637 | 282 |
283 bool DicomInstanceParameters::IsColor() const | |
284 { | |
285 Orthanc::PhotometricInterpretation photometric = | |
1642
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
286 GetImageInformation().GetPhotometricInterpretation(); |
1637 | 287 |
288 return (photometric != Orthanc::PhotometricInterpretation_Monochrome1 && | |
289 photometric != Orthanc::PhotometricInterpretation_Monochrome2); | |
290 } | |
291 | |
292 | |
1636 | 293 void DicomInstanceParameters::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image, |
294 bool useDouble) const | |
746 | 295 { |
296 if (image.GetFormat() != Orthanc::PixelFormat_Float32) | |
297 { | |
298 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
299 } | |
1141
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
300 |
1636 | 301 double factor = data_.doseGridScaling_; |
1141
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
302 double offset = 0.0; |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
303 |
1636 | 304 if (data_.hasRescale_) |
746 | 305 { |
1636 | 306 factor *= data_.rescaleSlope_; |
307 offset = data_.rescaleIntercept_; | |
1141
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
308 } |
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
309 |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
310 if (!LinearAlgebra::IsNear(factor, 1) || |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
311 !LinearAlgebra::IsNear(offset, 0)) |
1141
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
312 { |
746 | 313 const unsigned int width = image.GetWidth(); |
314 const unsigned int height = image.GetHeight(); | |
315 | |
316 for (unsigned int y = 0; y < height; y++) | |
317 { | |
318 float* p = reinterpret_cast<float*>(image.GetRow(y)); | |
319 | |
320 if (useDouble) | |
321 { | |
322 // Slower, accurate implementation using double | |
323 for (unsigned int x = 0; x < width; x++, p++) | |
324 { | |
325 double value = static_cast<double>(*p); | |
1141
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
326 *p = static_cast<float>(value * factor + offset); |
746 | 327 } |
328 } | |
329 else | |
330 { | |
331 // Fast, approximate implementation using float | |
332 for (unsigned int x = 0; x < width; x++, p++) | |
333 { | |
1141
7681f3943748
Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents:
1091
diff
changeset
|
334 *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset); |
746 | 335 } |
336 } | |
337 } | |
338 } | |
339 } | |
340 | |
341 double DicomInstanceParameters::GetRescaleIntercept() const | |
342 { | |
343 if (data_.hasRescale_) | |
344 { | |
345 return data_.rescaleIntercept_; | |
346 } | |
347 else | |
348 { | |
956
a7351ad54960
Made IsContextLost automatically set the flag by checking with the emscripten
Benjamin Golinvaux <bgo@osimis.io>
parents:
949
diff
changeset
|
349 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_"; |
746 | 350 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
351 } | |
352 } | |
353 | |
354 | |
355 double DicomInstanceParameters::GetRescaleSlope() const | |
356 { | |
357 if (data_.hasRescale_) | |
358 { | |
359 return data_.rescaleSlope_; | |
360 } | |
361 else | |
362 { | |
956
a7351ad54960
Made IsContextLost automatically set the flag by checking with the emscripten
Benjamin Golinvaux <bgo@osimis.io>
parents:
949
diff
changeset
|
363 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_"; |
746 | 364 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
365 } | |
366 } | |
367 | |
368 | |
1637 | 369 Orthanc::PixelFormat DicomInstanceParameters::GetExpectedPixelFormat() const |
370 { | |
371 if (GetSopClassUid() == SopClassUid_RTDose) | |
372 { | |
373 switch (GetImageInformation().GetBitsStored()) | |
374 { | |
375 case 16: | |
376 return Orthanc::PixelFormat_Grayscale16; | |
377 | |
378 case 32: | |
379 return Orthanc::PixelFormat_Grayscale32; | |
380 | |
381 default: | |
382 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
383 } | |
384 } | |
385 else if (IsColor()) | |
386 { | |
387 return Orthanc::PixelFormat_RGB24; | |
388 } | |
389 else if (GetImageInformation().IsSigned()) | |
390 { | |
391 return Orthanc::PixelFormat_SignedGrayscale16; | |
392 } | |
393 else | |
394 { | |
395 return Orthanc::PixelFormat_Grayscale16; // Rough guess | |
396 } | |
397 } | |
398 | |
399 | |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
400 size_t DicomInstanceParameters::GetPresetWindowingsCount() const |
746 | 401 { |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
402 assert(data_.presetWindowingCenters_.size() == data_.presetWindowingWidths_.size()); |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
403 return data_.presetWindowingCenters_.size(); |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
404 } |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
405 |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
406 |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
407 float DicomInstanceParameters::GetPresetWindowingCenter(size_t i) const |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
408 { |
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
409 if (i < GetPresetWindowingsCount()) |
746 | 410 { |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
411 return static_cast<float>(data_.presetWindowingCenters_[i]); |
746 | 412 } |
413 else | |
414 { | |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
415 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
746 | 416 } |
417 } | |
418 | |
419 | |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
420 float DicomInstanceParameters::GetPresetWindowingWidth(size_t i) const |
746 | 421 { |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
422 if (i < GetPresetWindowingsCount()) |
746 | 423 { |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
424 return static_cast<float>(data_.presetWindowingWidths_[i]); |
746 | 425 } |
426 else | |
427 { | |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
428 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
746 | 429 } |
430 } | |
431 | |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
432 |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
433 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
434 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1291
diff
changeset
|
435 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32, |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
436 pixelData.GetWidth(), |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
437 pixelData.GetHeight(), |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
438 false)); |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
439 Orthanc::ImageProcessing::Convert(*converted, pixelData); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
440 |
1287
8e82fdc6200e
Heavy (temporary) logging in the path that leads
Benjamin Golinvaux <bgo@osimis.io>
parents:
1270
diff
changeset
|
441 |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
442 // Correct rescale slope/intercept if need be |
1636 | 443 //ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32)); |
444 ApplyRescaleAndDoseScaling(*converted, false); | |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
445 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
446 return converted.release(); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
447 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
448 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
449 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
450 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
451 (const Orthanc::ImageAccessor& pixelData) const |
746 | 452 { |
1353
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
453 // { |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
454 // const Orthanc::ImageAccessor& source = pixelData; |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
455 // const void* sourceBuffer = source.GetConstBuffer(); |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
456 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer); |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
457 // int sourceWidth = source.GetWidth(); |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
458 // int sourceHeight = source.GetHeight(); |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
459 // int sourcePitch = source.GetPitch(); |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
460 |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
461 // // TODO: turn error into trace below |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
462 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:" |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
463 // << " W = " << sourceWidth << " H = " << sourceHeight |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
464 // << " P = " << sourcePitch << " B = " << sourceBufferInt |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
465 // << " B % 4 == " << sourceBufferInt % 4; |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
466 // } |
af65bce18951
Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents:
1300
diff
changeset
|
467 |
746 | 468 assert(sizeof(float) == 4); |
469 | |
470 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat(); | |
471 | |
472 if (sourceFormat != GetExpectedPixelFormat()) | |
473 { | |
474 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat); | |
475 } | |
476 | |
477 if (sourceFormat == Orthanc::PixelFormat_RGB24) | |
478 { | |
479 // This is the case of a color image. No conversion has to be done. | |
480 return new ColorTextureSceneLayer(pixelData); | |
481 } | |
482 else | |
483 { | |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
484 // This is the case of a grayscale frame. Convert it to Float32. |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1291
diff
changeset
|
485 std::unique_ptr<FloatTextureSceneLayer> texture; |
746 | 486 |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
487 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
746 | 488 { |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
489 texture.reset(new FloatTextureSceneLayer(pixelData)); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
490 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
491 else |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
492 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1291
diff
changeset
|
493 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
746 | 494 texture.reset(new FloatTextureSceneLayer(*converted)); |
495 } | |
496 | |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
497 if (GetPresetWindowingsCount() > 0) |
746 | 498 { |
1677
51bab5188a13
start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1646
diff
changeset
|
499 texture->SetCustomWindowing(GetPresetWindowingCenter(0), GetPresetWindowingWidth(0)); |
746 | 500 } |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
501 |
1642
5cc589bfb385
lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1639
diff
changeset
|
502 switch (GetImageInformation().GetPhotometricInterpretation()) |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
503 { |
1634
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
504 case Orthanc::PhotometricInterpretation_Monochrome1: |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
505 texture->SetInverted(true); |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
506 break; |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
507 |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
508 case Orthanc::PhotometricInterpretation_Monochrome2: |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
509 texture->SetInverted(false); |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
510 break; |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
511 |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
512 default: |
a4418a489e86
improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1598
diff
changeset
|
513 break; |
1206
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
514 } |
c93a6218f0cd
Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents:
1141
diff
changeset
|
515 |
746 | 516 return texture.release(); |
517 } | |
518 } | |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
519 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
520 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
521 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
522 (const Orthanc::ImageAccessor& pixelData) const |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
523 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1291
diff
changeset
|
524 std::unique_ptr<FloatTextureSceneLayer> texture; |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
525 |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
526 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32) |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
527 { |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
528 return new LookupTableTextureSceneLayer(pixelData); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
529 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
530 else |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
531 { |
1298
8a0a62189f46
replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1291
diff
changeset
|
532 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData)); |
768
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
533 return new LookupTableTextureSceneLayer(*converted); |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
534 } |
55411e7da2f7
LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
762
diff
changeset
|
535 } |
980
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
536 |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
537 |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
538 unsigned int DicomInstanceParameters::GetIndexInSeries() const |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
539 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
540 if (data_.hasIndexInSeries_) |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
541 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
542 return data_.indexInSeries_; |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
543 } |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
544 else |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
545 { |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
546 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_"; |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
547 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
548 } |
8e497a4e3d96
DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
956
diff
changeset
|
549 } |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
550 |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
551 |
1636 | 552 double DicomInstanceParameters::ApplyRescale(double value) const |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
553 { |
1636 | 554 double factor = data_.doseGridScaling_; |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
555 double offset = 0.0; |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
556 |
1636 | 557 if (data_.hasRescale_) |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
558 { |
1636 | 559 factor *= data_.rescaleSlope_; |
560 offset = data_.rescaleIntercept_; | |
1159
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
561 } |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
562 |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
563 return (value * factor + offset); |
acb399643945
DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1141
diff
changeset
|
564 } |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
565 |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
566 |
1636 | 567 bool DicomInstanceParameters::ComputeRegularSpacing(double& spacing) const |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
568 { |
1636 | 569 if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
570 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
571 return false; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
572 } |
1636 | 573 else if (data_.frameOffsets_.size() == 1) |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
574 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
575 spacing = 1; // Edge case: RT-DOSE with one single frame |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
576 return true; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
577 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
578 else |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
579 { |
1636 | 580 assert(data_.frameOffsets_.size() == GetNumberOfFrames()); |
581 | |
582 spacing = std::abs(data_.frameOffsets_[1] - data_.frameOffsets_[0]); | |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
583 |
1636 | 584 for (size_t i = 1; i + 1 < data_.frameOffsets_.size(); i++) |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
585 { |
1636 | 586 double s = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i]; |
1161
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
587 if (!LinearAlgebra::IsNear(spacing, s, 0.001)) |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
588 { |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
589 return false; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
590 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
591 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
592 |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
593 return true; |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
594 } |
19b1c8caade4
fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1159
diff
changeset
|
595 } |
746 | 596 } |