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annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1639:5cdc5b98f14d

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 10 Nov 2020 16:41:11 +0100
parents d569effcd433
children 5cc589bfb385
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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) 2017-2020 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Lesser General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Lesser General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Lesser General Public
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18 * License along with this program. If not, see
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19 * <http://www.gnu.org/licenses/>.
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20 **/
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21
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22
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23 #include "DicomInstanceParameters.h"
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24
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25 #include "../Scene2D/ColorTextureSceneLayer.h"
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26 #include "../Scene2D/FloatTextureSceneLayer.h"
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27 #include "../Toolbox/GeometryToolbox.h"
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28 #include "../Toolbox/ImageToolbox.h"
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29
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30 #include <Images/Image.h>
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31 #include <Images/ImageProcessing.h>
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32 #include <Logging.h>
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33 #include <OrthancException.h>
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34 #include <Toolbox.h>
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35
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36
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37 namespace OrthancStone
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38 {
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39 static void ExtractFrameOffsets(Vector& target,
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40 const Orthanc::DicomMap& dicom,
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41 unsigned int numberOfFrames)
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42 {
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43 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html
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44
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45 std::string increment;
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47 if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false))
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48 {
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49 Orthanc::Toolbox::ToUpperCase(increment);
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50
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51 // This is the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR)
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52 if (increment != "3004,000C")
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53 {
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54 LOG(WARNING) << "Bad value for the FrameIncrementPointer tags in a multiframe image";
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55 target.resize(0);
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56 return;
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57 }
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58 }
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59
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60 if (!LinearAlgebra::ParseVector(target, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) ||
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61 target.size() != numberOfFrames)
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62 {
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63 LOG(INFO) << "The frame offset information is missing in a multiframe image";
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64
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65 // DO NOT use ".clear()" here, as the "Vector" class doesn't behave like std::vector!
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66 target.resize(0);
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67 }
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68 }
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70
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71 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom) :
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72 imageInformation_(dicom)
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73 {
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74 if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) ||
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75 !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) ||
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76 !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false))
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77 {
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78 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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79 }
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80
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81 std::string s;
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82 if (dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false))
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83 {
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84 sopClassUid_ = StringToSopClassUid(s);
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85 }
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86 else
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87 {
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88 sopClassUid_ = SopClassUid_Other;
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89 }
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90
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91 uint32_t n;
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92 if (dicom.ParseUnsignedInteger32(n, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
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93 {
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94 numberOfFrames_ = n;
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95 }
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96 else
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97 {
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98 numberOfFrames_ = 1;
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99 }
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100
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101 if (!dicom.HasTag(Orthanc::DICOM_TAG_COLUMNS) ||
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102 !dicom.GetValue(Orthanc::DICOM_TAG_COLUMNS).ParseFirstUnsignedInteger(width_))
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103 {
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104 width_ = 0;
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105 }
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106
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107 if (!dicom.HasTag(Orthanc::DICOM_TAG_ROWS) ||
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108 !dicom.GetValue(Orthanc::DICOM_TAG_ROWS).ParseFirstUnsignedInteger(height_))
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109 {
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110 height_ = 0;
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111 }
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112
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113 if (!dicom.ParseDouble(sliceThickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS))
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114 {
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115 sliceThickness_ = 100.0 * std::numeric_limits<double>::epsilon();
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116 }
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117
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118 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom);
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119
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120 std::string position, orientation;
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121 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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122 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
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123 {
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124 geometry_ = CoordinateSystem3D(position, orientation);
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125 }
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126
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127 // Must be AFTER setting "numberOfFrames_"
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128 if (numberOfFrames_ > 1)
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129 {
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130 ExtractFrameOffsets(frameOffsets_, dicom, numberOfFrames_);
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131 }
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132 else
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133 {
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134 frameOffsets_.resize(0);
5cdc5b98f14d cppcheck
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diff changeset
135 }
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diff changeset
136
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137 if (sopClassUid_ == SopClassUid_RTDose)
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parents:
diff changeset
138 {
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diff changeset
139 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002);
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140
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diff changeset
141 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false))
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parents: 1027
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142 {
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143 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_;
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diff changeset
144 doseUnits_.clear();
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parents: 1027
diff changeset
145 }
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146 }
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parents:
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147
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148 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) &&
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149 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE))
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150 {
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151 if (sopClassUid_ == SopClassUid_RTDose)
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152 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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153 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_;
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154 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES
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155 hasRescale_ = false;
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diff changeset
156 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
157 else
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
158 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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159 hasRescale_ = true;
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160 }
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161
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162 }
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163 else
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parents:
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164 {
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165 hasRescale_ = false;
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166 }
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167
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168 if (dicom.ParseDouble(doseGridScaling_, Orthanc::DICOM_TAG_DOSE_GRID_SCALING))
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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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 if (sopClassUid_ == SopClassUid_RTDose)
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Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
171 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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diff changeset
172 LOG(INFO) << "DOSE HAS DoseGridScaling: doseGridScaling_ = " << doseGridScaling_;
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Benjamin Golinvaux <bgo@osimis.io>
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173 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
174 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
175 else
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
176 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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177 doseGridScaling_ = 1.0;
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178 if (sopClassUid_ == SopClassUid_RTDose)
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
179 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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180 LOG(ERROR) << "Tag DoseGridScaling (0x3004, 0x000e) is missing in " << sopInstanceUid_ << " doseGridScaling_ will be set to 1.0";
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181 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
182 }
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183
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184 Vector c, w;
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185 if (LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) &&
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186 LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) &&
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187 c.size() > 0 &&
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188 w.size() > 0)
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189 {
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190 hasDefaultWindowing_ = true;
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191 defaultWindowingCenter_ = static_cast<float>(c[0]);
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192 defaultWindowingWidth_ = static_cast<float>(w[0]);
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parents:
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193 }
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parents:
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194 else
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parents:
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195 {
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196 hasDefaultWindowing_ = false;
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197 defaultWindowingCenter_ = 0;
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198 defaultWindowingWidth_ = 0;
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199 }
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200
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201 // This computes the "IndexInSeries" metadata from Orthanc (check
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202 // out "Orthanc::ServerIndex::Store()")
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203 hasIndexInSeries_ = (
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
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204 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) ||
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205 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX));
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206 }
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parents:
diff changeset
207
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208
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209 CoordinateSystem3D DicomInstanceParameters::GetFrameGeometry(unsigned int frame) const
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210 {
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211 if (frame >= data_.numberOfFrames_)
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212 {
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213 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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214 }
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215 else if (data_.frameOffsets_.empty())
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216 {
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217 return data_.geometry_;
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218 }
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219 else
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diff changeset
220 {
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221 assert(data_.frameOffsets_.size() == data_.numberOfFrames_);
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222
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223 return CoordinateSystem3D(
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224 data_.geometry_.GetOrigin() + data_.frameOffsets_[frame] * data_.geometry_.GetNormal(),
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225 data_.geometry_.GetAxisX(),
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226 data_.geometry_.GetAxisY());
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227 }
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parents:
diff changeset
228 }
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parents:
diff changeset
229
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diff changeset
230
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diff changeset
231 bool DicomInstanceParameters::IsPlaneWithinSlice(unsigned int frame,
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232 const CoordinateSystem3D& plane) const
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233 {
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diff changeset
234 if (frame >= data_.numberOfFrames_)
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parents:
diff changeset
235 {
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236 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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237 }
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diff changeset
238
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239 CoordinateSystem3D tmp = data_.geometry_;
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240
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diff changeset
241 if (frame != 0)
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parents:
diff changeset
242 {
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243 tmp = GetFrameGeometry(frame);
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diff changeset
244 }
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parents:
diff changeset
245
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diff changeset
246 double distance;
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diff changeset
247
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248 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) &&
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249 distance <= data_.sliceThickness_ / 2.0);
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parents:
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250 }
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diff changeset
251
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diff changeset
252
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253 bool DicomInstanceParameters::IsColor() const
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diff changeset
254 {
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255 Orthanc::PhotometricInterpretation photometric =
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256 data_.imageInformation_.GetPhotometricInterpretation();
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diff changeset
257
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parents: 1636
diff changeset
258 return (photometric != Orthanc::PhotometricInterpretation_Monochrome1 &&
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259 photometric != Orthanc::PhotometricInterpretation_Monochrome2);
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parents: 1636
diff changeset
260 }
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parents: 1636
diff changeset
261
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parents: 1636
diff changeset
262
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diff changeset
263 void DicomInstanceParameters::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image,
Sebastien Jodogne <s.jodogne@gmail.com>
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264 bool useDouble) const
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parents:
diff changeset
265 {
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266 if (image.GetFormat() != Orthanc::PixelFormat_Float32)
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parents:
diff changeset
267 {
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268 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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parents:
diff changeset
269 }
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270
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271 double factor = data_.doseGridScaling_;
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272 double offset = 0.0;
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273
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diff changeset
274 if (data_.hasRescale_)
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275 {
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276 factor *= data_.rescaleSlope_;
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277 offset = data_.rescaleIntercept_;
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parents: 1091
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278 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
279
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parents: 1598
diff changeset
280 if (!LinearAlgebra::IsNear(factor, 1) ||
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parents: 1598
diff changeset
281 !LinearAlgebra::IsNear(offset, 0))
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parents: 1091
diff changeset
282 {
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283 const unsigned int width = image.GetWidth();
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parents:
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284 const unsigned int height = image.GetHeight();
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parents:
diff changeset
285
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parents:
diff changeset
286 for (unsigned int y = 0; y < height; y++)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
287 {
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288 float* p = reinterpret_cast<float*>(image.GetRow(y));
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parents:
diff changeset
289
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
290 if (useDouble)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
291 {
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parents:
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292 // Slower, accurate implementation using double
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parents:
diff changeset
293 for (unsigned int x = 0; x < width; x++, p++)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
294 {
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parents:
diff changeset
295 double value = static_cast<double>(*p);
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parents: 1091
diff changeset
296 *p = static_cast<float>(value * factor + offset);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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297 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
298 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
299 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
300 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
301 // Fast, approximate implementation using float
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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302 for (unsigned int x = 0; x < width; x++, p++)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
303 {
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parents: 1091
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304 *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset);
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parents:
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305 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
306 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
307 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
308 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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309 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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310
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311 double DicomInstanceParameters::GetRescaleIntercept() const
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312 {
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parents:
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313 if (data_.hasRescale_)
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parents:
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314 {
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parents:
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315 return data_.rescaleIntercept_;
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parents:
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316 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
317 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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318 {
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319 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_";
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320 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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321 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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322 }
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parents:
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323
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parents:
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324
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parents:
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325 double DicomInstanceParameters::GetRescaleSlope() const
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326 {
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parents:
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327 if (data_.hasRescale_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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328 {
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329 return data_.rescaleSlope_;
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parents:
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330 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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331 else
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parents:
diff changeset
332 {
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parents: 949
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333 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_";
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334 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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parents:
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335 }
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parents:
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336 }
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parents:
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337
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338
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parents: 1636
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339 Orthanc::PixelFormat DicomInstanceParameters::GetExpectedPixelFormat() const
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340 {
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parents: 1636
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341 if (GetSopClassUid() == SopClassUid_RTDose)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1636
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342 {
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parents: 1636
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343 switch (GetImageInformation().GetBitsStored())
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parents: 1636
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344 {
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parents: 1636
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345 case 16:
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parents: 1636
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346 return Orthanc::PixelFormat_Grayscale16;
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parents: 1636
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347
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parents: 1636
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348 case 32:
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349 return Orthanc::PixelFormat_Grayscale32;
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parents: 1636
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350
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parents: 1636
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351 default:
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parents: 1636
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352 return Orthanc::PixelFormat_Grayscale16; // Rough guess
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parents: 1636
diff changeset
353 }
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parents: 1636
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354 }
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parents: 1636
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355 else if (IsColor())
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parents: 1636
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356 {
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parents: 1636
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357 return Orthanc::PixelFormat_RGB24;
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parents: 1636
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358 }
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parents: 1636
diff changeset
359 else if (GetImageInformation().IsSigned())
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parents: 1636
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360 {
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parents: 1636
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361 return Orthanc::PixelFormat_SignedGrayscale16;
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parents: 1636
diff changeset
362 }
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parents: 1636
diff changeset
363 else
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parents: 1636
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364 {
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parents: 1636
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365 return Orthanc::PixelFormat_Grayscale16; // Rough guess
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parents: 1636
diff changeset
366 }
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parents: 1636
diff changeset
367 }
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parents: 1636
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368
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parents: 1636
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369
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370 float DicomInstanceParameters::GetDefaultWindowingCenter() const
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parents:
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371 {
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parents:
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372 if (data_.hasDefaultWindowing_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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373 {
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parents:
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374 return data_.defaultWindowingCenter_;
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parents:
diff changeset
375 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
376 else
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parents:
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377 {
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parents: 1455
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378 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingCenter(): no default windowing";
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379 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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parents:
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380 }
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parents:
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381 }
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parents:
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382
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parents:
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383
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parents:
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384 float DicomInstanceParameters::GetDefaultWindowingWidth() const
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parents:
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385 {
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parents:
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386 if (data_.hasDefaultWindowing_)
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parents:
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387 {
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388 return data_.defaultWindowingWidth_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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389 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
390 else
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parents:
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391 {
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parents: 1455
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392 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingWidth(): no default windowing";
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parents:
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393 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
394 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
395 }
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parents:
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396
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parents:
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397
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parents: 762
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398 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const
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parents: 762
diff changeset
399 {
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parents: 1291
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400 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32,
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parents: 1598
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401 pixelData.GetWidth(),
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parents: 1598
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402 pixelData.GetHeight(),
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parents: 1598
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403 false));
768
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parents: 762
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404 Orthanc::ImageProcessing::Convert(*converted, pixelData);
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parents: 762
diff changeset
405
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parents: 1270
diff changeset
406
768
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parents: 762
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407 // Correct rescale slope/intercept if need be
1636
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parents: 1635
diff changeset
408 //ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32));
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parents: 1635
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409 ApplyRescaleAndDoseScaling(*converted, false);
768
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parents: 762
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410
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parents: 762
diff changeset
411 return converted.release();
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parents: 762
diff changeset
412 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
413
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parents: 762
diff changeset
414
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parents: 762
diff changeset
415 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture
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parents: 762
diff changeset
416 (const Orthanc::ImageAccessor& pixelData) const
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parents:
diff changeset
417 {
1353
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diff changeset
418 // {
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419 // const Orthanc::ImageAccessor& source = pixelData;
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420 // const void* sourceBuffer = source.GetConstBuffer();
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421 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer);
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parents: 1300
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422 // int sourceWidth = source.GetWidth();
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parents: 1300
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423 // int sourceHeight = source.GetHeight();
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parents: 1300
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424 // int sourcePitch = source.GetPitch();
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parents: 1300
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425
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parents: 1300
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426 // // TODO: turn error into trace below
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parents: 1300
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427 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:"
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parents: 1300
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428 // << " W = " << sourceWidth << " H = " << sourceHeight
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parents: 1300
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429 // << " P = " << sourcePitch << " B = " << sourceBufferInt
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parents: 1300
diff changeset
430 // << " B % 4 == " << sourceBufferInt % 4;
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parents: 1300
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431 // }
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parents: 1300
diff changeset
432
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parents:
diff changeset
433 assert(sizeof(float) == 4);
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parents:
diff changeset
434
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parents:
diff changeset
435 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat();
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
436
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
437 if (sourceFormat != GetExpectedPixelFormat())
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
438 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
439 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
440 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
441
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
442 if (sourceFormat == Orthanc::PixelFormat_RGB24)
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
443 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
444 // This is the case of a color image. No conversion has to be done.
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
445 return new ColorTextureSceneLayer(pixelData);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
446 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
447 else
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
448 {
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
449 // This is the case of a grayscale frame. Convert it to Float32.
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
450 std::unique_ptr<FloatTextureSceneLayer> texture;
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
451
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
452 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
453 {
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
454 texture.reset(new FloatTextureSceneLayer(pixelData));
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
455 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
456 else
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
457 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
458 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
459 texture.reset(new FloatTextureSceneLayer(*converted));
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
460 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
461
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
462 if (data_.hasDefaultWindowing_)
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
463 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
464 texture->SetCustomWindowing(data_.defaultWindowingCenter_,
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
465 data_.defaultWindowingWidth_);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
466 }
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
467
1634
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
468 switch (data_.imageInformation_.GetPhotometricInterpretation())
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
469 {
1634
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
470 case Orthanc::PhotometricInterpretation_Monochrome1:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
471 texture->SetInverted(true);
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
472 break;
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
473
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
474 case Orthanc::PhotometricInterpretation_Monochrome2:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
475 texture->SetInverted(false);
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
476 break;
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
477
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
478 default:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
479 break;
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
480 }
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
481
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
482 return texture.release();
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
483 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
484 }
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
485
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
486
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
487 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
488 (const Orthanc::ImageAccessor& pixelData) const
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
489 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
490 std::unique_ptr<FloatTextureSceneLayer> texture;
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
491
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
492 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
493 {
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
494 return new LookupTableTextureSceneLayer(pixelData);
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
495 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
496 else
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
497 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
498 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
499 return new LookupTableTextureSceneLayer(*converted);
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
500 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
501 }
980
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
502
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
503
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
504 unsigned int DicomInstanceParameters::GetIndexInSeries() const
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
505 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
506 if (data_.hasIndexInSeries_)
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
507 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
508 return data_.indexInSeries_;
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
509 }
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
510 else
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
511 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
512 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_";
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
513 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
514 }
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
515 }
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
516
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
517
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
518 double DicomInstanceParameters::ApplyRescale(double value) const
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
519 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
520 double factor = data_.doseGridScaling_;
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
521 double offset = 0.0;
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
522
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
523 if (data_.hasRescale_)
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
524 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
525 factor *= data_.rescaleSlope_;
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
526 offset = data_.rescaleIntercept_;
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
527 }
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
528
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
529 return (value * factor + offset);
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
530 }
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
531
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
532
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
533 bool DicomInstanceParameters::ComputeRegularSpacing(double& spacing) const
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
534 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
535 if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
536 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
537 return false;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
538 }
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
539 else if (data_.frameOffsets_.size() == 1)
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
540 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
541 spacing = 1; // Edge case: RT-DOSE with one single frame
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
542 return true;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
543 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
544 else
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
545 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
546 assert(data_.frameOffsets_.size() == GetNumberOfFrames());
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
547
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
548 spacing = std::abs(data_.frameOffsets_[1] - data_.frameOffsets_[0]);
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
549
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
550 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
551 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
552 double s = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i];
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
553 if (!LinearAlgebra::IsNear(spacing, s, 0.001))
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
554 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
555 return false;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
556 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
557 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
558
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
559 return true;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
560 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
561 }
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
562 }