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annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1635:1a714e21ea7c

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start refactoring DicomInstanceParameters
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 10 Nov 2020 16:08:44 +0100
parents a4418a489e86
children d1e0b08b809d
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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 void DicomInstanceParameters::Data::ExtractFrameOffsets(const Orthanc::DicomMap& dicom)
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40 {
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41 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html
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42
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43 std::string increment;
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44
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45 if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false))
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46 {
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47 Orthanc::Toolbox::ToUpperCase(increment);
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48
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49 // This is the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR)
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50 if (increment != "3004,000C")
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51 {
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52 LOG(WARNING) << "Bad value for the FrameIncrementPointer tags in a multiframe image";
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53 frameOffsets_.resize(0);
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54 return;
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55 }
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56 }
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57
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58 if (!LinearAlgebra::ParseVector(frameOffsets_, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) ||
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59 frameOffsets_.size() != numberOfFrames_)
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60 {
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61 LOG(INFO) << "The frame offset information is missing in a multiframe image";
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62
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63 // DO NOT use ".clear()" here, as the "Vector" class doesn't behave like std::vector!
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64 frameOffsets_.resize(0);
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65 }
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66 }
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68
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69 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom) :
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70 imageInformation_(dicom)
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71 {
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72 if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) ||
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73 !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) ||
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74 !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false))
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75 {
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76 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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77 }
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78
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79 std::string s;
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80 if (dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false))
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81 {
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82 sopClassUid_ = StringToSopClassUid(s);
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83 }
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84 else
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85 {
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86 sopClassUid_ = SopClassUid_Other;
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87 }
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88
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89 uint32_t n;
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90 if (dicom.ParseUnsignedInteger32(n, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
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91 {
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92 numberOfFrames_ = n;
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93 }
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94 else
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95 {
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96 numberOfFrames_ = 1;
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97 }
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98
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99 if (!dicom.HasTag(Orthanc::DICOM_TAG_COLUMNS) ||
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100 !dicom.GetValue(Orthanc::DICOM_TAG_COLUMNS).ParseFirstUnsignedInteger(width_))
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101 {
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102 width_ = 0;
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103 }
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104
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105 if (!dicom.HasTag(Orthanc::DICOM_TAG_ROWS) ||
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106 !dicom.GetValue(Orthanc::DICOM_TAG_ROWS).ParseFirstUnsignedInteger(height_))
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107 {
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108 height_ = 0;
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109 }
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110
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111 if (!dicom.ParseDouble(sliceThickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS))
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112 {
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113 sliceThickness_ = 100.0 * std::numeric_limits<double>::epsilon();
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114 }
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115
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116 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom);
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117
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118 std::string position, orientation;
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119 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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120 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
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121 {
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122 geometry_ = CoordinateSystem3D(position, orientation);
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123 }
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124
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125 // Must be AFTER setting "numberOfFrames_"
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126 ExtractFrameOffsets(dicom);
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127
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128 if (sopClassUid_ == SopClassUid_RTDose)
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129 {
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130 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002);
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diff changeset
131
5a18e6a395bc Added DoseUnit tag retrieval to DicomInstanceParameters
Benjamin Golinvaux <bgo@osimis.io>
parents: 1027
diff changeset
132 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false))
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parents: 1027
diff changeset
133 {
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parents: 1091
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134 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_;
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diff changeset
135 doseUnits_.clear();
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parents: 1027
diff changeset
136 }
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137 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
138
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parents:
diff changeset
139 isColor_ = (imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome1 &&
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parents:
diff changeset
140 imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome2);
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parents:
diff changeset
141
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parents:
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142 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) &&
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parents:
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143 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE))
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parents:
diff changeset
144 {
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parents: 1091
diff changeset
145 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
146 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
147 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_;
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parents: 1091
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148 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES
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parents: 1091
diff changeset
149 hasRescale_ = false;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
150 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
151 else
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
152 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
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153 hasRescale_ = true;
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154 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
155
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156 }
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parents:
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157 else
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parents:
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158 {
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159 hasRescale_ = false;
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parents:
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160 }
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parents:
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161
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parents: 1091
diff changeset
162 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
163 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
164 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
165 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
166 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
167 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
168 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
169 else
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
170 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
171 doseGridScaling_ = 1.0;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
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172 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
173 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
174 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
175 }
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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parents: 1091
diff changeset
177
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178 Vector c, w;
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179 if (LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) &&
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180 LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) &&
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181 c.size() > 0 &&
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182 w.size() > 0)
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183 {
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184 hasDefaultWindowing_ = true;
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185 defaultWindowingCenter_ = static_cast<float>(c[0]);
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parents:
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186 defaultWindowingWidth_ = static_cast<float>(w[0]);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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187 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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188 else
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parents:
diff changeset
189 {
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parents:
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190 hasDefaultWindowing_ = false;
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parents: 1091
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191 defaultWindowingCenter_ = 0;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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192 defaultWindowingWidth_ = 0;
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193 }
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parents:
diff changeset
194
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195 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16; // Rough guess
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196
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197 if (sopClassUid_ == SopClassUid_RTDose)
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parents:
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198 {
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parents:
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199 switch (imageInformation_.GetBitsStored())
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parents:
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200 {
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parents:
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201 case 16:
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202 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
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parents:
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203 break;
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parents:
diff changeset
204
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parents:
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205 case 32:
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parents:
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206 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale32;
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parents:
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207 break;
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parents:
diff changeset
208
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parents:
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209 default:
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210 break;
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parents:
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211 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
212 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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213 else if (isColor_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
214 {
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215 expectedPixelFormat_ = Orthanc::PixelFormat_RGB24;
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parents:
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216 }
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parents:
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217 else if (imageInformation_.IsSigned())
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parents:
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218 {
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219 expectedPixelFormat_ = Orthanc::PixelFormat_SignedGrayscale16;
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parents:
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220 }
980
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221
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222 // This computes the "IndexInSeries" metadata from Orthanc (check
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223 // out "Orthanc::ServerIndex::Store()")
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224 hasIndexInSeries_ = (
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
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parents: 956
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225 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) ||
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226 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX));
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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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230 CoordinateSystem3D DicomInstanceParameters::Data::GetFrameGeometry(unsigned int frame) const
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231 {
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232 if (frame >= numberOfFrames_)
746
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parents:
diff changeset
233 {
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parents:
diff changeset
234 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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parents:
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235 }
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parents: 1598
diff changeset
236 else if (frameOffsets_.empty())
746
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parents:
diff changeset
237 {
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238 return geometry_;
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parents: 1598
diff changeset
239 }
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parents: 1598
diff changeset
240 else
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parents: 1598
diff changeset
241 {
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parents: 1634
diff changeset
242 assert(frameOffsets_.size() == numberOfFrames_);
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243
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parents:
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244 return CoordinateSystem3D(
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parents:
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245 geometry_.GetOrigin() + frameOffsets_[frame] * geometry_.GetNormal(),
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parents:
diff changeset
246 geometry_.GetAxisX(),
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parents:
diff changeset
247 geometry_.GetAxisY());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
248 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
249 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
250
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parents:
diff changeset
251
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parents:
diff changeset
252 bool DicomInstanceParameters::Data::IsPlaneWithinSlice(unsigned int frame,
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parents:
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253 const CoordinateSystem3D& plane) const
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parents:
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254 {
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parents: 1634
diff changeset
255 if (frame >= numberOfFrames_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
256 {
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parents:
diff changeset
257 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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parents:
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258 }
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parents:
diff changeset
259
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parents:
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260 CoordinateSystem3D tmp = geometry_;
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parents:
diff changeset
261
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parents:
diff changeset
262 if (frame != 0)
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parents:
diff changeset
263 {
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parents:
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264 tmp = GetFrameGeometry(frame);
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parents:
diff changeset
265 }
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parents:
diff changeset
266
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parents:
diff changeset
267 double distance;
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parents:
diff changeset
268
757
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parents: 746
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269 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) &&
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270 distance <= sliceThickness_ / 2.0);
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parents:
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271 }
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272
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273 void DicomInstanceParameters::Data::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image,
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acb399643945 DicomInstanceParameters::ApplyRescale()
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274 bool useDouble) const
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275 {
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276 if (image.GetFormat() != Orthanc::PixelFormat_Float32)
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277 {
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278 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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279 }
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diff changeset
280
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diff changeset
281 double factor = doseGridScaling_;
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282 double offset = 0.0;
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283
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284 if (hasRescale_)
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285 {
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286 factor *= rescaleSlope_;
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287 offset = rescaleIntercept_;
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288 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
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289
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290 if (!LinearAlgebra::IsNear(factor, 1) ||
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291 !LinearAlgebra::IsNear(offset, 0))
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292 {
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293 const unsigned int width = image.GetWidth();
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294 const unsigned int height = image.GetHeight();
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295
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296 for (unsigned int y = 0; y < height; y++)
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297 {
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298 float* p = reinterpret_cast<float*>(image.GetRow(y));
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299
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300 if (useDouble)
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parents:
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301 {
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302 // Slower, accurate implementation using double
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303 for (unsigned int x = 0; x < width; x++, p++)
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304 {
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305 double value = static_cast<double>(*p);
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306 *p = static_cast<float>(value * factor + offset);
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307 }
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308 }
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309 else
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310 {
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311 // Fast, approximate implementation using float
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312 for (unsigned int x = 0; x < width; x++, p++)
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313 {
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314 *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset);
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315 }
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316 }
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parents:
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317 }
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318 }
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319 }
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320
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321 double DicomInstanceParameters::GetRescaleIntercept() const
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322 {
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323 if (data_.hasRescale_)
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parents:
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324 {
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325 return data_.rescaleIntercept_;
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326 }
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327 else
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parents:
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328 {
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329 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_";
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330 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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331 }
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332 }
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333
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334
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335 double DicomInstanceParameters::GetRescaleSlope() const
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336 {
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337 if (data_.hasRescale_)
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338 {
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339 return data_.rescaleSlope_;
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340 }
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341 else
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342 {
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343 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_";
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344 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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345 }
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346 }
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347
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348
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349 float DicomInstanceParameters::GetDefaultWindowingCenter() const
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350 {
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351 if (data_.hasDefaultWindowing_)
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parents:
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352 {
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353 return data_.defaultWindowingCenter_;
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parents:
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354 }
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parents:
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355 else
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parents:
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356 {
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357 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingCenter(): no default windowing";
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358 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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359 }
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parents:
diff changeset
360 }
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parents:
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361
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parents:
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362
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363 float DicomInstanceParameters::GetDefaultWindowingWidth() const
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parents:
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364 {
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parents:
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365 if (data_.hasDefaultWindowing_)
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parents:
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366 {
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367 return data_.defaultWindowingWidth_;
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parents:
diff changeset
368 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
369 else
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parents:
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370 {
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parents: 1455
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371 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingWidth(): no default windowing";
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372 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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373 }
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parents:
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374 }
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parents:
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375
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parents:
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376
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377 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const
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parents: 762
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378 {
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379 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32,
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380 pixelData.GetWidth(),
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381 pixelData.GetHeight(),
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382 false));
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383 Orthanc::ImageProcessing::Convert(*converted, pixelData);
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parents: 762
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384
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parents: 1270
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385
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parents: 762
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386 // Correct rescale slope/intercept if need be
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387 //data_.ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32));
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388 data_.ApplyRescaleAndDoseScaling(*converted, false);
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389
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390 return converted.release();
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parents: 762
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391 }
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parents: 762
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392
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parents: 762
diff changeset
393
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394 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture
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395 (const Orthanc::ImageAccessor& pixelData) const
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396 {
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397 // {
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398 // const Orthanc::ImageAccessor& source = pixelData;
af65bce18951 Dummy commented debug block
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399 // const void* sourceBuffer = source.GetConstBuffer();
af65bce18951 Dummy commented debug block
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400 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer);
af65bce18951 Dummy commented debug block
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401 // int sourceWidth = source.GetWidth();
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parents: 1300
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402 // int sourceHeight = source.GetHeight();
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parents: 1300
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403 // int sourcePitch = source.GetPitch();
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parents: 1300
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404
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parents: 1300
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405 // // TODO: turn error into trace below
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parents: 1300
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406 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:"
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parents: 1300
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407 // << " W = " << sourceWidth << " H = " << sourceHeight
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parents: 1300
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408 // << " P = " << sourcePitch << " B = " << sourceBufferInt
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parents: 1300
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409 // << " B % 4 == " << sourceBufferInt % 4;
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410 // }
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parents: 1300
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411
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412 assert(sizeof(float) == 4);
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parents:
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413
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parents:
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414 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat();
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parents:
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415
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parents:
diff changeset
416 if (sourceFormat != GetExpectedPixelFormat())
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parents:
diff changeset
417 {
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418 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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parents:
diff changeset
419 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
420
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
421 if (sourceFormat == Orthanc::PixelFormat_RGB24)
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
422 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
423 // 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
424 return new ColorTextureSceneLayer(pixelData);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
425 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
426 else
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
427 {
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
428 // 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
429 std::unique_ptr<FloatTextureSceneLayer> texture;
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
430
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
431 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
432 {
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
433 texture.reset(new FloatTextureSceneLayer(pixelData));
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
434 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
435 else
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
436 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
437 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
438 texture.reset(new FloatTextureSceneLayer(*converted));
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
439 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
440
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
441 if (data_.hasDefaultWindowing_)
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
442 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
443 texture->SetCustomWindowing(data_.defaultWindowingCenter_,
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
444 data_.defaultWindowingWidth_);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
445 }
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
446
1634
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
447 switch (data_.imageInformation_.GetPhotometricInterpretation())
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
448 {
1634
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
449 case Orthanc::PhotometricInterpretation_Monochrome1:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
450 texture->SetInverted(true);
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
451 break;
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
452
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
453 case Orthanc::PhotometricInterpretation_Monochrome2:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
454 texture->SetInverted(false);
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
455 break;
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
456
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
457 default:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
458 break;
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
459 }
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
460
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
461 return texture.release();
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
462 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
463 }
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
464
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
465
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
466 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
467 (const Orthanc::ImageAccessor& pixelData) const
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
468 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
469 std::unique_ptr<FloatTextureSceneLayer> texture;
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
470
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
471 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
472 {
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
473 return new LookupTableTextureSceneLayer(pixelData);
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
474 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
475 else
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
476 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
477 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
478 return new LookupTableTextureSceneLayer(*converted);
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
479 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
480 }
980
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
481
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
482
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
483 unsigned int DicomInstanceParameters::GetIndexInSeries() const
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
484 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
485 if (data_.hasIndexInSeries_)
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
486 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
487 return data_.indexInSeries_;
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
488 }
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
489 else
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
490 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
491 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_";
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
492 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
493 }
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
494 }
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
495
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
496
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
497 double DicomInstanceParameters::Data::ApplyRescale(double value) const
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
498 {
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
499 double factor = doseGridScaling_;
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
500 double offset = 0.0;
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
501
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
502 if (hasRescale_)
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
503 {
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
504 factor *= rescaleSlope_;
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
505 offset = rescaleIntercept_;
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
506 }
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
507
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
508 return (value * factor + offset);
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
509 }
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
510
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
511
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
512 bool DicomInstanceParameters::Data::ComputeRegularSpacing(double& spacing) const
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
513 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
514 if (frameOffsets_.size() == 0) // Not a RT-DOSE
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
515 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
516 return false;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
517 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
518 else if (frameOffsets_.size() == 1)
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
519 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
520 spacing = 1; // Edge case: RT-DOSE with one single frame
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
521 return true;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
522 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
523 else
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
524 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
525 spacing = std::abs(frameOffsets_[1] - frameOffsets_[0]);
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
526
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
527 for (size_t i = 1; i + 1 < frameOffsets_.size(); i++)
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
528 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
529 double s = frameOffsets_[i + 1] - frameOffsets_[i];
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
530 if (!LinearAlgebra::IsNear(spacing, s, 0.001))
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 return false;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
533 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
534 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
535
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
536 return true;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
537 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
538 }
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
539 }