Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 2169:fe5406abd43f

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added separate class Windowing
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 21 Oct 2024 15:40:34 +0200
parents 16c01cc201e7
children 8e3c403cc643
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1 /**
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2 * Stone of Orthanc
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2023 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU Lesser General Public License
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10 * as published by the Free Software Foundation, either version 3 of
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11 * the License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * Lesser General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU Lesser General Public
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19 * License along with this program. If not, see
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20 * <http://www.gnu.org/licenses/>.
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21 **/
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22
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23
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24 #include "DicomInstanceParameters.h"
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25
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26 #include "../Scene2D/ColorTextureSceneLayer.h"
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27 #include "../Scene2D/FloatTextureSceneLayer.h"
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28 #include "GeometryToolbox.h"
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29 #include "ImageToolbox.h"
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30
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31 #include <Images/Image.h>
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32 #include <Images/ImageProcessing.h>
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33 #include <Logging.h>
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34 #include <OrthancException.h>
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35 #include <Toolbox.h>
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36
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37
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38 namespace OrthancStone
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39 {
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40 static void ExtractFrameOffsets(Vector& target,
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41 const Orthanc::DicomMap& dicom,
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42 unsigned int numberOfFrames)
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43 {
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44 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html
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46 std::string increment;
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47
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48 if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false))
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49 {
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50 Orthanc::Toolbox::ToUpperCase(increment);
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51
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52 // We only support volumes where the FrameIncrementPointer (0028,0009) (required) contains
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53 // the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR)
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54 if (increment != "3004,000C")
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55 {
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56 LOG(WARNING) << "Bad value for the FrameIncrementPointer tags in a multiframe image";
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57 target.resize(0);
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58 return;
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59 }
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60 }
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61
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62 if (!LinearAlgebra::ParseVector(target, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) ||
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63 target.size() != numberOfFrames)
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64 {
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65 LOG(ERROR) << "The frame offset information (GridFrameOffsetVector (3004,000C)) is missing in a multiframe image";
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66
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67 // DO NOT use ".clear()" here, as the "Vector" class doesn't behave like std::vector!
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68 target.resize(0);
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69 }
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70 }
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71
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72
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73 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom)
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74 {
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75 if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) ||
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76 !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) ||
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77 !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false))
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78 {
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79 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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80 }
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81
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82 std::string s;
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83 if (dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false))
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84 {
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85 sopClassUid_ = StringToSopClassUid(s);
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86 }
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87 else
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88 {
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89 sopClassUid_ = SopClassUid_Other;
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90 }
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91
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92 uint32_t n;
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93 if (dicom.ParseUnsignedInteger32(n, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
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94 {
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95 hasNumberOfFrames_ = true;
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96 numberOfFrames_ = n;
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97 }
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98 else
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99 {
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100 hasNumberOfFrames_ = false;
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101 numberOfFrames_ = 1;
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102 }
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103
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104 if (!dicom.HasTag(Orthanc::DICOM_TAG_COLUMNS) ||
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105 !dicom.GetValue(Orthanc::DICOM_TAG_COLUMNS).ParseFirstUnsignedInteger(width_))
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106 {
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107 width_ = 0;
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108 }
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109
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110 if (!dicom.HasTag(Orthanc::DICOM_TAG_ROWS) ||
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111 !dicom.GetValue(Orthanc::DICOM_TAG_ROWS).ParseFirstUnsignedInteger(height_))
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112 {
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113 height_ = 0;
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114 }
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115
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116
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117 if (dicom.ParseDouble(sliceThickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS))
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118 {
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119 hasSliceThickness_ = true;
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120 }
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121 else
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122 {
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123 hasSliceThickness_ = false;
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124
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125 if (numberOfFrames_ > 1)
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126 {
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127 LOG(INFO) << "The (non-madatory) slice thickness information is missing in a multiframe image";
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128 }
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129 }
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130
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131 hasPixelSpacing_ = GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom);
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parents:
diff changeset
132
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parents:
diff changeset
133 std::string position, orientation;
994
1f74bc3459ba fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 980
diff changeset
134 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
135 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
136 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
137 geometry_ = CoordinateSystem3D(position, orientation);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
138 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
139
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parents: 1634
diff changeset
140 // Must be AFTER setting "numberOfFrames_"
1639
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1637
diff changeset
141 if (numberOfFrames_ > 1)
5cdc5b98f14d cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1637
diff changeset
142 {
5cdc5b98f14d cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1637
diff changeset
143 ExtractFrameOffsets(frameOffsets_, dicom, numberOfFrames_);
5cdc5b98f14d cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1637
diff changeset
144 }
1634
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
145
746
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
146 if (sopClassUid_ == SopClassUid_RTDose)
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
147 {
1091
5a18e6a395bc Added DoseUnit tag retrieval to DicomInstanceParameters
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parents: 1027
diff changeset
148 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
149
5a18e6a395bc Added DoseUnit tag retrieval to DicomInstanceParameters
Benjamin Golinvaux <bgo@osimis.io>
parents: 1027
diff changeset
150 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
151 {
1141
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parents: 1091
diff changeset
152 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_;
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parents: 1598
diff changeset
153 doseUnits_.clear();
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parents: 1027
diff changeset
154 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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155 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
156
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parents:
diff changeset
157 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) &&
d716bfb3e07c reorganization
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parents:
diff changeset
158 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE))
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parents:
diff changeset
159 {
1141
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Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
160 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
161 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
162 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
163 // 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
164 hasRescale_ = false;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
165 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
166 else
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
167 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
168 hasRescale_ = true;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
169 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
170
746
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parents:
diff changeset
171 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
172 else
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parents:
diff changeset
173 {
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parents:
diff changeset
174 hasRescale_ = false;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
175 }
d716bfb3e07c reorganization
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parents:
diff changeset
176
1141
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
177 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
178 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
179 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
180 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
181 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
182 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
183 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
184 else
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
185 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
186 doseGridScaling_ = 1.0;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
187 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
188 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
189 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
190 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
191 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
192
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parents: 2124
diff changeset
193
fe5406abd43f added separate class Windowing
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parents: 2124
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194 windowingPresets_.clear();
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parents: 2124
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195
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parents: 2124
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196 Vector centers, widths;
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diff changeset
197
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parents: 2124
diff changeset
198 if (LinearAlgebra::ParseVector(centers, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) &&
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parents: 2124
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199 LinearAlgebra::ParseVector(widths, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH))
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200 {
2169
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parents: 2124
diff changeset
201 if (centers.size() == widths.size())
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parents: 1646
diff changeset
202 {
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203 windowingPresets_.resize(centers.size());
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parents: 2124
diff changeset
204
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parents: 2124
diff changeset
205 for (size_t i = 0; i < centers.size(); i++)
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diff changeset
206 {
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parents: 2124
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207 windowingPresets_[i] = Windowing(centers[i], widths[i]);
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parents: 2124
diff changeset
208 }
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parents: 1646
diff changeset
209 }
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parents: 1646
diff changeset
210 else
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parents: 1646
diff changeset
211 {
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212 LOG(ERROR) << "Mismatch in the number of preset windowing widths/centers, ignoring this";
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213 }
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parents:
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214 }
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parents: 1646
diff changeset
215
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216 // This computes the "IndexInSeries" metadata from Orthanc (check
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217 // out "Orthanc::ServerIndex::Store()")
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218 hasIndexInSeries_ = (
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
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219 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) ||
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
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220 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX));
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parents: 1642
diff changeset
221
4e14735e98f8 preparing to remove FrameExtent
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parents: 1642
diff changeset
222 if (!dicom.LookupStringValue(
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parents: 1642
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223 frameOfReferenceUid_, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, false))
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parents: 1642
diff changeset
224 {
4e14735e98f8 preparing to remove FrameExtent
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225 frameOfReferenceUid_.clear();
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parents: 1642
diff changeset
226 }
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227
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parents: 1822
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228 if (!dicom.HasTag(Orthanc::DICOM_TAG_INSTANCE_NUMBER) ||
2789b4b0e0a8 DicomInstanceParameters::HasNumberOfFrames() and DicomInstanceParameters::GetInstanceNumber()
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parents: 1822
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229 !dicom.GetValue(Orthanc::DICOM_TAG_INSTANCE_NUMBER).ParseInteger32(instanceNumber_))
2789b4b0e0a8 DicomInstanceParameters::HasNumberOfFrames() and DicomInstanceParameters::GetInstanceNumber()
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parents: 1822
diff changeset
230 {
2789b4b0e0a8 DicomInstanceParameters::HasNumberOfFrames() and DicomInstanceParameters::GetInstanceNumber()
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parents: 1822
diff changeset
231 instanceNumber_ = 0;
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parents: 1822
diff changeset
232 }
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parents:
diff changeset
233 }
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parents:
diff changeset
234
d716bfb3e07c reorganization
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parents:
diff changeset
235
2076
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parents: 2075
diff changeset
236 double DicomInstanceParameters::GetSliceThickness() const
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parents: 2075
diff changeset
237 {
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diff changeset
238 if (data_.hasSliceThickness_)
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parents: 2075
diff changeset
239 {
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diff changeset
240 return data_.sliceThickness_;
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parents: 2075
diff changeset
241 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
242 else
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
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parents: 2075
diff changeset
243 {
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
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parents: 2075
diff changeset
244 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
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parents: 2075
diff changeset
245 }
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
246 }
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
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parents: 2075
diff changeset
247
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
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parents: 2075
diff changeset
248
1642
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parents: 1639
diff changeset
249 const Orthanc::DicomImageInformation& DicomInstanceParameters::GetImageInformation() const
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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parents: 1639
diff changeset
250 {
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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parents: 1639
diff changeset
251 assert(tags_.get() != NULL);
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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parents: 1639
diff changeset
252
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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parents: 1639
diff changeset
253 if (imageInformation_.get() == NULL)
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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parents: 1639
diff changeset
254 {
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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255 const_cast<DicomInstanceParameters&>(*this).imageInformation_.
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parents: 1639
diff changeset
256 reset(new Orthanc::DicomImageInformation(GetTags()));
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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parents: 1639
diff changeset
257
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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parents: 1639
diff changeset
258 assert(imageInformation_->GetWidth() == GetWidth());
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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parents: 1639
diff changeset
259 assert(imageInformation_->GetHeight() == GetHeight());
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
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parents: 1639
diff changeset
260 assert(imageInformation_->GetNumberOfFrames() == GetNumberOfFrames());
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1639
diff changeset
261 }
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1639
diff changeset
262
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1639
diff changeset
263 assert(imageInformation_.get() != NULL);
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1639
diff changeset
264 return *imageInformation_;
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1639
diff changeset
265 }
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1639
diff changeset
266
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1639
diff changeset
267
1636
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parents: 1635
diff changeset
268 CoordinateSystem3D DicomInstanceParameters::GetFrameGeometry(unsigned int frame) const
746
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parents:
diff changeset
269 {
1636
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parents: 1635
diff changeset
270 if (frame >= data_.numberOfFrames_)
746
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
271 {
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parents:
diff changeset
272 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
273 }
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
274 else if (data_.frameOffsets_.empty())
746
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
275 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
276 return data_.geometry_;
1634
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
277 }
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
278 else
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
279 {
1636
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parents: 1635
diff changeset
280 assert(data_.frameOffsets_.size() == data_.numberOfFrames_);
746
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parents:
diff changeset
281
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
282 return CoordinateSystem3D(
1636
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parents: 1635
diff changeset
283 data_.geometry_.GetOrigin() + data_.frameOffsets_[frame] * data_.geometry_.GetNormal(),
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
284 data_.geometry_.GetAxisX(),
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
285 data_.geometry_.GetAxisY());
746
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
286 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
287 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
288
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
289
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
290 bool DicomInstanceParameters::IsPlaneWithinSlice(unsigned int frame,
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
291 const CoordinateSystem3D& plane) const
746
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
292 {
1636
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parents: 1635
diff changeset
293 if (frame >= data_.numberOfFrames_)
746
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
294 {
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parents:
diff changeset
295 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
296 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
297
1636
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parents: 1635
diff changeset
298 CoordinateSystem3D tmp = data_.geometry_;
746
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parents:
diff changeset
299
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
300 if (frame != 0)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
301 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
302 tmp = GetFrameGeometry(frame);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
303 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
304
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
305 double distance;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
306
757
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 746
diff changeset
307 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) &&
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
308 distance <= data_.sliceThickness_ / 2.0);
746
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
309 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
310
1637
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parents: 1636
diff changeset
311
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
312 bool DicomInstanceParameters::IsColor() const
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
313 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
314 Orthanc::PhotometricInterpretation photometric =
1642
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1639
diff changeset
315 GetImageInformation().GetPhotometricInterpretation();
1637
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
316
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
317 return (photometric != Orthanc::PhotometricInterpretation_Monochrome1 &&
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
318 photometric != Orthanc::PhotometricInterpretation_Monochrome2);
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
319 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
320
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
321
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
322 void DicomInstanceParameters::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
323 bool useDouble) const
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
324 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
325 if (image.GetFormat() != Orthanc::PixelFormat_Float32)
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
326 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
327 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
328 }
1141
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
329
1924
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
330 double scaling = data_.doseGridScaling_;
1141
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
331 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
332
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
333 if (data_.hasRescale_)
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
334 {
1924
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
335 scaling *= data_.rescaleSlope_;
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
336 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
337 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
338
1924
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
339 Orthanc::ImageProcessing::ShiftScale2(image, offset, scaling, false);
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
340 }
1924
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
341
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
342
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
343 double DicomInstanceParameters::GetRescaleIntercept() const
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
344 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
345 if (data_.hasRescale_)
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
346 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
347 return data_.rescaleIntercept_;
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
348 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
349 else
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
350 {
956
a7351ad54960 Made IsContextLost automatically set the flag by checking with the emscripten
Benjamin Golinvaux <bgo@osimis.io>
parents: 949
diff changeset
351 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_";
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
352 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
353 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
354 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
355
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
356
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
357 double DicomInstanceParameters::GetRescaleSlope() const
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
358 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
359 if (data_.hasRescale_)
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
360 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
361 return data_.rescaleSlope_;
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
362 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
363 else
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
364 {
956
a7351ad54960 Made IsContextLost automatically set the flag by checking with the emscripten
Benjamin Golinvaux <bgo@osimis.io>
parents: 949
diff changeset
365 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_";
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
366 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
367 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
368 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
369
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
370
1637
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
371 Orthanc::PixelFormat DicomInstanceParameters::GetExpectedPixelFormat() const
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
372 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
373 if (GetSopClassUid() == SopClassUid_RTDose)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
374 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
375 switch (GetImageInformation().GetBitsStored())
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
376 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
377 case 16:
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
378 return Orthanc::PixelFormat_Grayscale16;
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
379
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
380 case 32:
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
381 return Orthanc::PixelFormat_Grayscale32;
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
382
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
383 default:
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
384 return Orthanc::PixelFormat_Grayscale16; // Rough guess
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
385 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
386 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
387 else if (IsColor())
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
388 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
389 return Orthanc::PixelFormat_RGB24;
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
390 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
391 else if (GetImageInformation().IsSigned())
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
392 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
393 return Orthanc::PixelFormat_SignedGrayscale16;
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
394 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
395 else
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
396 {
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
397 return Orthanc::PixelFormat_Grayscale16; // Rough guess
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
398 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
399 }
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
400
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
diff changeset
401
2169
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
402 Windowing DicomInstanceParameters::GetFallbackWindowing() const
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
403 {
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
404 double a, b;
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
405 if (tags_->ParseDouble(a, Orthanc::DICOM_TAG_SMALLEST_IMAGE_PIXEL_VALUE) &&
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
406 tags_->ParseDouble(b, Orthanc::DICOM_TAG_LARGEST_IMAGE_PIXEL_VALUE))
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
407 {
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
408 const double center = (a + b) / 2.0f;
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
409 const double width = (b - a);
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
410 return Windowing(center, width);
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
411 }
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
412
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
413 // Added in Stone Web viewer > 2.5
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
414 uint32_t bitsStored, pixelRepresentation;
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
415 if (tags_->ParseUnsignedInteger32(bitsStored, Orthanc::DICOM_TAG_BITS_STORED) &&
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
416 tags_->ParseUnsignedInteger32(pixelRepresentation, Orthanc::DICOM_TAG_PIXEL_REPRESENTATION))
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
417 {
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
418 const bool isSigned = (pixelRepresentation != 0);
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
419 const float maximum = powf(2.0, bitsStored);
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
420 return Windowing(isSigned ? 0.0f : maximum / 2.0f, maximum);
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
421 }
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
422 else
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
423 {
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
424 // Cannot infer a suitable windowing from the available tags
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
425 return Windowing();
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
426 }
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
427 }
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
428
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
429
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
430 size_t DicomInstanceParameters::GetWindowingPresetsCount() const
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
431 {
2169
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
432 return data_.windowingPresets_.size();
1677
51bab5188a13 start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1646
diff changeset
433 }
51bab5188a13 start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1646
diff changeset
434
51bab5188a13 start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1646
diff changeset
435
2169
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
436 Windowing DicomInstanceParameters::GetWindowingPreset(size_t i) const
1677
51bab5188a13 start multiple preset windowings
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1646
diff changeset
437 {
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
438 if (i < GetWindowingPresetsCount())
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
439 {
2169
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
440 return data_.windowingPresets_[i];
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
441 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
442 else
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
443 {
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
444 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
445 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
446 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
447
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
448
2169
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
449 Windowing DicomInstanceParameters::GetWindowingPresetsUnion() const
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
450 {
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
451 assert(tags_.get() != NULL);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
452 size_t s = GetWindowingPresetsCount();
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
453
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
454 if (s > 0)
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
455 {
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
456 // Use the largest windowing given all the preset windowings
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
457 // that are available in the DICOM tags
2169
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
458 double low, high;
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
459 GetWindowingPreset(0).GetBounds(low, high);
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
460
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
461 for (size_t i = 1; i < s; i++)
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
462 {
2169
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
463 double a, b;
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
464 GetWindowingPreset(i).GetBounds(a, b);
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
465 low = std::min(low, a);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
466 high = std::max(high, b);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
467 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
468
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
469 assert(low <= high);
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
470
2169
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
471 if (!LinearAlgebra::IsNear(low, high))
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
472 {
2169
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
473 const double center = (low + high) / 2.0f;
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
474 const double width = (high - low);
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
475 return Windowing(center, width);
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
476 }
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
477 }
2169
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
478
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
479 // No preset, or presets with an empty range
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
480 return GetFallbackWindowing();
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
481 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
482
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
483
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
484 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
485 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
486 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
487 pixelData.GetWidth(),
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
488 pixelData.GetHeight(),
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
489 false));
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
490 Orthanc::ImageProcessing::Convert(*converted, pixelData);
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
491
1287
8e82fdc6200e Heavy (temporary) logging in the path that leads
Benjamin Golinvaux <bgo@osimis.io>
parents: 1270
diff changeset
492
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
493 // Correct rescale slope/intercept if need be
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
494 //ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32));
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
495 ApplyRescaleAndDoseScaling(*converted, false);
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
496
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
497 return converted.release();
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
498 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
499
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
500
1919
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
501 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture(
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
502 const Orthanc::ImageAccessor& pixelData) const
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
503 {
1353
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
504 // {
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
505 // const Orthanc::ImageAccessor& source = pixelData;
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
506 // const void* sourceBuffer = source.GetConstBuffer();
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
507 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer);
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
508 // int sourceWidth = source.GetWidth();
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
509 // int sourceHeight = source.GetHeight();
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
510 // int sourcePitch = source.GetPitch();
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
511
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
512 // // TODO: turn error into trace below
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
513 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:"
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
514 // << " W = " << sourceWidth << " H = " << sourceHeight
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
515 // << " P = " << sourcePitch << " B = " << sourceBufferInt
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
516 // << " B % 4 == " << sourceBufferInt % 4;
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
517 // }
af65bce18951 Dummy commented debug block
Benjamin Golinvaux <bgo@osimis.io>
parents: 1300
diff changeset
518
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
519 assert(sizeof(float) == 4);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
520
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
521 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat();
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
522
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
523 if (sourceFormat != GetExpectedPixelFormat())
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
524 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
525 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
526 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
527
1911
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
528 std::unique_ptr<TextureBaseSceneLayer> texture;
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
529
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
530 if (sourceFormat == Orthanc::PixelFormat_RGB24)
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
531 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
532 // This is the case of a color image. No conversion has to be done.
1911
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
533 texture.reset(new ColorTextureSceneLayer(pixelData));
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
534 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
535 else
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
536 {
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
537 // This is the case of a grayscale frame. Convert it to Float32.
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
538 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
539 {
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
540 texture.reset(new FloatTextureSceneLayer(pixelData));
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
541 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
542 else
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
543 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
544 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
545 texture.reset(new FloatTextureSceneLayer(*converted));
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
546 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
547
1911
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
548 FloatTextureSceneLayer& floatTexture = dynamic_cast<FloatTextureSceneLayer&>(*texture);
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
549
1679
5b8b88e5bfd6 successfully running unit tests in WebAssembly
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1677
diff changeset
550 if (GetWindowingPresetsCount() > 0)
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
551 {
2169
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
552 Windowing preset = GetWindowingPreset(0);
fe5406abd43f added separate class Windowing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2124
diff changeset
553 floatTexture.SetCustomWindowing(preset.GetCenter(), preset.GetWidth());
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
554 }
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
555
1642
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1639
diff changeset
556 switch (GetImageInformation().GetPhotometricInterpretation())
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
557 {
1634
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
558 case Orthanc::PhotometricInterpretation_Monochrome1:
1911
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
559 floatTexture.SetInverted(true);
1634
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
560 break;
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
561
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
562 case Orthanc::PhotometricInterpretation_Monochrome2:
1911
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
563 floatTexture.SetInverted(false);
1634
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
564 break;
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
565
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
566 default:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
567 break;
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
568 }
1911
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
569 }
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
570
1911
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
571 if (HasPixelSpacing())
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
572 {
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
573 texture->SetPixelSpacing(GetPixelSpacingX(), GetPixelSpacingY());
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
574 }
1911
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
575
898774b4e02d DicomInstanceParameters::CreateTexture() now sets pixel spacing
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1871
diff changeset
576 return texture.release();
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
577 }
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
578
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
579
1919
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
580 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture(
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
581 const Orthanc::ImageAccessor& pixelData) const
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
582 {
1919
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
583 std::unique_ptr<LookupTableTextureSceneLayer> texture;
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
584
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
585 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
586 {
1919
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
587 texture.reset(new LookupTableTextureSceneLayer(pixelData));
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
588 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
589 else
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
590 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
591 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
1919
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
592 texture.reset(new LookupTableTextureSceneLayer(*converted));
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
593 }
1919
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
594
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
595 if (HasPixelSpacing())
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
596 {
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
597 texture->SetPixelSpacing(GetPixelSpacingX(), GetPixelSpacingY());
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
598 }
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
599
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
600 return texture.release();
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
601 }
980
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
602
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
603
1919
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
604 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateOverlayTexture(
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
605 int originX,
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
606 int originY,
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
607 const Orthanc::ImageAccessor& overlay) const
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
608 {
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
609 if (overlay.GetFormat() != Orthanc::PixelFormat_Grayscale8)
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
610 {
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
611 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
612 }
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
613
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
614 std::unique_ptr<LookupTableTextureSceneLayer> texture(CreateLookupTableTexture(overlay));
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
615
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
616 texture->SetOrigin(static_cast<double>(originX - 1) * texture->GetPixelSpacingX(),
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
617 static_cast<double>(originY - 1) * texture->GetPixelSpacingY());
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
618
1924
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
619 std::vector<uint8_t> lut(4 * 256);
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
620 for (size_t i = 0; i < 256; i++)
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
621 {
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
622 if (i < 127)
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
623 {
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
624 // Black pixels are converted to transparent pixels
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
625 lut[4 * i] = 0;
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
626 lut[4 * i + 1] = 0;
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
627 lut[4 * i + 2] = 0;
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
628 lut[4 * i + 3] = 0; // alpha
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
629 }
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
630 else
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
631 {
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
632 // White pixels are converted to opaque white
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
633 lut[4 * i] = 255;
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
634 lut[4 * i + 1] = 255;
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
635 lut[4 * i + 2] = 255;
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
636 lut[4 * i + 3] = 255; // alpha
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
637 }
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
638 }
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
639
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
640 texture->SetLookupTable(lut);
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
641
1919
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
642 return texture.release();
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
643 }
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
644
ed4831e08961 added DicomInstanceParameters::CreateOverlayTexture()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1911
diff changeset
645
980
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
646 unsigned int DicomInstanceParameters::GetIndexInSeries() const
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
647 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
648 if (data_.hasIndexInSeries_)
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
649 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
650 return data_.indexInSeries_;
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
651 }
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
652 else
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
653 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
654 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_";
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
655 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
656 }
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
657 }
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
658
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
659
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
660 double DicomInstanceParameters::ApplyRescale(double value) const
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
661 {
1924
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
662 double scaling = data_.doseGridScaling_;
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
663 double offset = 0.0;
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
664
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
665 if (data_.hasRescale_)
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
666 {
1924
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
667 scaling *= data_.rescaleSlope_;
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
668 offset = data_.rescaleIntercept_;
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
669 }
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
670
1924
f4050908c6bc display of overlays
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1919
diff changeset
671 return (value * scaling + offset);
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
672 }
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
673
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
674
2076
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
675 bool DicomInstanceParameters::ComputeFrameOffsetsSpacing(double& spacing) const
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
676 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
677 if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
678 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
679 return false;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
680 }
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
681 else if (data_.frameOffsets_.size() == 1)
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
682 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
683 spacing = 1; // Edge case: RT-DOSE with one single frame
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
684 return true;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
685 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
686 else
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
687 {
2076
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
688 static double THRESHOLD = 0.001;
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
689
2076
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
690 if (data_.frameOffsets_.size() != GetNumberOfFrames())
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
691 {
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
692 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
693 }
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
694
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
695 double a = data_.frameOffsets_[1] - data_.frameOffsets_[0];
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
696
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
697 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
698 {
2076
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
699 double b = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i];
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
700 if (!LinearAlgebra::IsNear(a, b, THRESHOLD))
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
701 {
2076
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
702 LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: varying spacing)";
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
703 return false;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
704 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
705 }
2076
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
706
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
707 spacing = std::abs(a);
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
708
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
709 if (HasSliceThickness() &&
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
710 !LinearAlgebra::IsNear(spacing, GetSliceThickness(), THRESHOLD))
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
711 {
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
712 LOG(WARNING) << "SliceThickness and GridFrameOffsetVector (3004,000C) do not match";
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
713 }
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
714
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
715 return true;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
716 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
717 }
1822
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
718
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
719
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
720 void DicomInstanceParameters::SetPixelSpacing(double pixelSpacingX,
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
721 double pixelSpacingY)
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
722 {
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
723 data_.hasPixelSpacing_ = true;
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
724 data_.pixelSpacingX_ = pixelSpacingX;
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
725 data_.pixelSpacingY_ = pixelSpacingY;
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
726 }
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
727
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
728
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
729 static const Json::Value* LookupDicomWebSingleValue(const Json::Value& dicomweb,
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
730 const std::string& tag,
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
731 const std::string& vr)
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
732 {
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
733 static const char* const VALUE = "Value";
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
734 static const char* const VR = "vr";
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
735
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
736 if (dicomweb.type() == Json::objectValue &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
737 dicomweb.isMember(tag) &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
738 dicomweb[tag].type() == Json::objectValue &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
739 dicomweb[tag].isMember(VALUE) &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
740 dicomweb[tag].isMember(VR) &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
741 dicomweb[tag][VR].type() == Json::stringValue &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
742 dicomweb[tag][VR].asString() == vr &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
743 dicomweb[tag][VALUE].type() == Json::arrayValue &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
744 dicomweb[tag][VALUE].size() == 1u)
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
745 {
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
746 return &dicomweb[tag][VALUE][0];
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
747 }
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
748 else
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
749 {
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
750 return NULL;
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
751 }
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
752 }
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
753
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
754
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
755 void DicomInstanceParameters::EnrichUsingDicomWeb(const Json::Value& dicomweb)
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
756 {
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
757 /**
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
758 * Use DICOM tag "SequenceOfUltrasoundRegions" (0018,6011) in
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
759 * order to derive the pixel spacing on ultrasound (US) images
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
760 **/
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
761
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
762 if (!data_.hasPixelSpacing_)
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
763 {
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
764 const Json::Value* region = LookupDicomWebSingleValue(dicomweb, "00186011", "SQ");
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
765 if (region != NULL)
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
766 {
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
767 const Json::Value* physicalUnitsXDirection = LookupDicomWebSingleValue(*region, "00186024", "US");
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
768 const Json::Value* physicalUnitsYDirection = LookupDicomWebSingleValue(*region, "00186026", "US");
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
769 const Json::Value* physicalDeltaX = LookupDicomWebSingleValue(*region, "0018602C", "FD");
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
770 const Json::Value* physicalDeltaY = LookupDicomWebSingleValue(*region, "0018602E", "FD");
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
771
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
772 if (physicalUnitsXDirection != NULL &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
773 physicalUnitsYDirection != NULL &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
774 physicalDeltaX != NULL &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
775 physicalDeltaY != NULL &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
776 physicalUnitsXDirection->type() == Json::intValue &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
777 physicalUnitsYDirection->type() == Json::intValue &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
778 physicalUnitsXDirection->asInt() == 0x0003 && // Centimeters
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
779 physicalUnitsYDirection->asInt() == 0x0003 && // Centimeters
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
780 physicalDeltaX->isNumeric() &&
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
781 physicalDeltaY->isNumeric())
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
782 {
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
783 // Scene coordinates are expressed in millimeters => multiplication by 10
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
784 SetPixelSpacing(10.0 * physicalDeltaX->asDouble(),
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
785 10.0 * physicalDeltaY->asDouble());
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
786 }
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
787 }
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
788 }
0489fe25ce48 support of pixel spacing in ultrasound images from tag SequenceOfUltrasoundRegions
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1821
diff changeset
789 }
2076
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
790
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
791
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
792 CoordinateSystem3D DicomInstanceParameters::GetMultiFrameGeometry() const
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
793 {
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
794 if (data_.frameOffsets_.empty())
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
795 {
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
796 return data_.geometry_;
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
797 }
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
798 else
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
799 {
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
800 assert(data_.frameOffsets_.size() == data_.numberOfFrames_);
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
801
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
802 double lowest = data_.frameOffsets_[0];
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
803 for (size_t i = 1; i < data_.frameOffsets_.size(); i++)
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
804 {
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
805 lowest = std::min(lowest, data_.frameOffsets_[i]);
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
806 }
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
807
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
808 return CoordinateSystem3D(
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
809 data_.geometry_.GetOrigin() + lowest * data_.geometry_.GetNormal(),
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
810 data_.geometry_.GetAxisX(),
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
811 data_.geometry_.GetAxisY());
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
812 }
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
813 }
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
814
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
815
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
816 bool DicomInstanceParameters::IsReversedFrameOffsets() const
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
817 {
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
818 if (data_.frameOffsets_.size() < 2)
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
819 {
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
820 return false;
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
821 }
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
822 else
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
823 {
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
824 return (data_.frameOffsets_[0] > data_.frameOffsets_[1]);
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
825 }
990f396484b1 fix rendering of RT-DOSE with negative GridFrameOffsetVector
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2075
diff changeset
826 }
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
827 }