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annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1636:d1e0b08b809d

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 10 Nov 2020 16:20:22 +0100
parents 1a714e21ea7c
children d569effcd433
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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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69
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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 ExtractFrameOffsets(frameOffsets_, dicom, numberOfFrames_);
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129
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130 if (sopClassUid_ == SopClassUid_RTDose)
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131 {
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132 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002);
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133
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Benjamin Golinvaux <bgo@osimis.io>
parents: 1027
diff changeset
134 if (!dicom.LookupStringValue(doseUnits_, DICOM_TAG_DOSE_UNITS, false))
5a18e6a395bc Added DoseUnit tag retrieval to DicomInstanceParameters
Benjamin Golinvaux <bgo@osimis.io>
parents: 1027
diff changeset
135 {
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Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
136 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_;
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diff changeset
137 doseUnits_.clear();
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parents: 1027
diff changeset
138 }
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parents:
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139 }
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parents:
diff changeset
140
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parents:
diff changeset
141 isColor_ = (imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome1 &&
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parents:
diff changeset
142 imageInformation_.GetPhotometricInterpretation() != Orthanc::PhotometricInterpretation_Monochrome2);
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parents:
diff changeset
143
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parents:
diff changeset
144 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) &&
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
145 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE))
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parents:
diff changeset
146 {
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parents: 1091
diff changeset
147 if (sopClassUid_ == SopClassUid_RTDose)
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
148 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
149 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
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150 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
151 hasRescale_ = false;
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
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
153 else
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
154 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
155 hasRescale_ = true;
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Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
156 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
157
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158 }
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parents:
diff changeset
159 else
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parents:
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160 {
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parents:
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161 hasRescale_ = false;
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parents:
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162 }
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parents:
diff changeset
163
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parents: 1091
diff changeset
164 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
165 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
166 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
167 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
168 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
169 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
170 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
171 else
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
172 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
173 doseGridScaling_ = 1.0;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
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174 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
175 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
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176 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
177 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
Benjamin Golinvaux <bgo@osimis.io>
parents: 1091
diff changeset
178 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to
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parents: 1091
diff changeset
179
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180 Vector c, w;
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181 if (LinearAlgebra::ParseVector(c, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) &&
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182 LinearAlgebra::ParseVector(w, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH) &&
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183 c.size() > 0 &&
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184 w.size() > 0)
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185 {
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186 hasDefaultWindowing_ = true;
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187 defaultWindowingCenter_ = static_cast<float>(c[0]);
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188 defaultWindowingWidth_ = static_cast<float>(w[0]);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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189 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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190 else
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parents:
diff changeset
191 {
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parents:
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192 hasDefaultWindowing_ = false;
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parents: 1091
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193 defaultWindowingCenter_ = 0;
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194 defaultWindowingWidth_ = 0;
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195 }
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parents:
diff changeset
196
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197 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16; // Rough guess
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198
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199 if (sopClassUid_ == SopClassUid_RTDose)
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parents:
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200 {
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parents:
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201 switch (imageInformation_.GetBitsStored())
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parents:
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202 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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203 case 16:
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204 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale16;
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parents:
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205 break;
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parents:
diff changeset
206
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parents:
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207 case 32:
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208 expectedPixelFormat_ = Orthanc::PixelFormat_Grayscale32;
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parents:
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209 break;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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210
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parents:
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211 default:
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212 break;
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parents:
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213 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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214 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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215 else if (isColor_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
216 {
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217 expectedPixelFormat_ = Orthanc::PixelFormat_RGB24;
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parents:
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218 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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219 else if (imageInformation_.IsSigned())
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parents:
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220 {
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221 expectedPixelFormat_ = Orthanc::PixelFormat_SignedGrayscale16;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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222 }
980
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
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223
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
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224 // This computes the "IndexInSeries" metadata from Orthanc (check
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
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225 // out "Orthanc::ServerIndex::Store()")
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226 hasIndexInSeries_ = (
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
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parents: 956
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227 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) ||
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
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228 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX));
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229 }
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parents:
diff changeset
230
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parents:
diff changeset
231
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232 CoordinateSystem3D DicomInstanceParameters::GetFrameGeometry(unsigned int frame) const
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233 {
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parents: 1635
diff changeset
234 if (frame >= data_.numberOfFrames_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
235 {
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parents:
diff changeset
236 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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parents:
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237 }
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parents: 1635
diff changeset
238 else if (data_.frameOffsets_.empty())
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parents:
diff changeset
239 {
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parents: 1635
diff changeset
240 return data_.geometry_;
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parents: 1598
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241 }
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parents: 1598
diff changeset
242 else
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parents: 1598
diff changeset
243 {
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diff changeset
244 assert(data_.frameOffsets_.size() == data_.numberOfFrames_);
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245
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246 return CoordinateSystem3D(
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parents: 1635
diff changeset
247 data_.geometry_.GetOrigin() + data_.frameOffsets_[frame] * data_.geometry_.GetNormal(),
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parents: 1635
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248 data_.geometry_.GetAxisX(),
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249 data_.geometry_.GetAxisY());
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parents:
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250 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
251 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
252
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parents:
diff changeset
253
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parents: 1635
diff changeset
254 bool DicomInstanceParameters::IsPlaneWithinSlice(unsigned int frame,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
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255 const CoordinateSystem3D& plane) const
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parents:
diff changeset
256 {
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parents: 1635
diff changeset
257 if (frame >= data_.numberOfFrames_)
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parents:
diff changeset
258 {
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parents:
diff changeset
259 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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parents:
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260 }
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parents:
diff changeset
261
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parents: 1635
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262 CoordinateSystem3D tmp = data_.geometry_;
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parents:
diff changeset
263
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parents:
diff changeset
264 if (frame != 0)
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parents:
diff changeset
265 {
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266 tmp = GetFrameGeometry(frame);
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parents:
diff changeset
267 }
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parents:
diff changeset
268
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269 double distance;
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270
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271 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) &&
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272 distance <= data_.sliceThickness_ / 2.0);
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parents:
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273 }
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parents:
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274
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parents: 1635
diff changeset
275 void DicomInstanceParameters::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image,
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276 bool useDouble) const
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277 {
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278 if (image.GetFormat() != Orthanc::PixelFormat_Float32)
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279 {
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280 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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281 }
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282
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283 double factor = data_.doseGridScaling_;
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284 double offset = 0.0;
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parents: 1091
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285
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286 if (data_.hasRescale_)
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287 {
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288 factor *= data_.rescaleSlope_;
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289 offset = data_.rescaleIntercept_;
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290 }
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291
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292 if (!LinearAlgebra::IsNear(factor, 1) ||
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293 !LinearAlgebra::IsNear(offset, 0))
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294 {
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295 const unsigned int width = image.GetWidth();
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296 const unsigned int height = image.GetHeight();
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297
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298 for (unsigned int y = 0; y < height; y++)
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299 {
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300 float* p = reinterpret_cast<float*>(image.GetRow(y));
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301
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302 if (useDouble)
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303 {
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304 // Slower, accurate implementation using double
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305 for (unsigned int x = 0; x < width; x++, p++)
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306 {
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307 double value = static_cast<double>(*p);
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308 *p = static_cast<float>(value * factor + offset);
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309 }
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310 }
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311 else
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312 {
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313 // Fast, approximate implementation using float
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314 for (unsigned int x = 0; x < width; x++, p++)
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315 {
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316 *p = (*p) * static_cast<float>(factor) + static_cast<float>(offset);
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317 }
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318 }
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319 }
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parents:
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320 }
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321 }
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322
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323 double DicomInstanceParameters::GetRescaleIntercept() const
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324 {
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325 if (data_.hasRescale_)
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326 {
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327 return data_.rescaleIntercept_;
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328 }
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329 else
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330 {
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331 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_";
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332 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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333 }
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334 }
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335
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336
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337 double DicomInstanceParameters::GetRescaleSlope() const
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338 {
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339 if (data_.hasRescale_)
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340 {
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341 return data_.rescaleSlope_;
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342 }
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343 else
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344 {
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345 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_";
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346 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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347 }
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348 }
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349
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350
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351 float DicomInstanceParameters::GetDefaultWindowingCenter() const
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352 {
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353 if (data_.hasDefaultWindowing_)
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354 {
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355 return data_.defaultWindowingCenter_;
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356 }
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parents:
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357 else
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358 {
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359 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingCenter(): no default windowing";
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360 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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361 }
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362 }
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363
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364
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365 float DicomInstanceParameters::GetDefaultWindowingWidth() const
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366 {
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367 if (data_.hasDefaultWindowing_)
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parents:
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368 {
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369 return data_.defaultWindowingWidth_;
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370 }
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parents:
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371 else
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parents:
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372 {
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373 LOG(ERROR) << "DicomInstanceParameters::GetDefaultWindowingWidth(): no default windowing";
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374 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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375 }
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parents:
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376 }
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377
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378
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379 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const
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380 {
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381 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32,
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382 pixelData.GetWidth(),
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383 pixelData.GetHeight(),
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384 false));
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385 Orthanc::ImageProcessing::Convert(*converted, pixelData);
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parents: 762
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386
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parents: 1270
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387
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388 // Correct rescale slope/intercept if need be
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parents: 1635
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389 //ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32));
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390 ApplyRescaleAndDoseScaling(*converted, false);
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391
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392 return converted.release();
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parents: 762
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393 }
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parents: 762
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394
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parents: 762
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395
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396 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture
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397 (const Orthanc::ImageAccessor& pixelData) const
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398 {
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399 // {
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400 // const Orthanc::ImageAccessor& source = pixelData;
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401 // const void* sourceBuffer = source.GetConstBuffer();
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402 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer);
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403 // int sourceWidth = source.GetWidth();
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404 // int sourceHeight = source.GetHeight();
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parents: 1300
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405 // int sourcePitch = source.GetPitch();
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406
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407 // // TODO: turn error into trace below
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408 // LOG(ERROR) << "ConvertGrayscaleToFloat | source:"
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409 // << " W = " << sourceWidth << " H = " << sourceHeight
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410 // << " P = " << sourcePitch << " B = " << sourceBufferInt
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411 // << " B % 4 == " << sourceBufferInt % 4;
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412 // }
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parents: 1300
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413
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414 assert(sizeof(float) == 4);
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415
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416 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat();
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417
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418 if (sourceFormat != GetExpectedPixelFormat())
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419 {
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420 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
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421 }
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parents:
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422
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423 if (sourceFormat == Orthanc::PixelFormat_RGB24)
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parents:
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424 {
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425 // This is the case of a color image. No conversion has to be done.
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426 return new ColorTextureSceneLayer(pixelData);
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parents:
diff changeset
427 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
428 else
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
429 {
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
430 // 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
431 std::unique_ptr<FloatTextureSceneLayer> texture;
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 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
434 {
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
435 texture.reset(new FloatTextureSceneLayer(pixelData));
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
436 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
437 else
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
438 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
439 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
440 texture.reset(new FloatTextureSceneLayer(*converted));
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
441 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
442
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
443 if (data_.hasDefaultWindowing_)
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
444 {
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
445 texture->SetCustomWindowing(data_.defaultWindowingCenter_,
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
446 data_.defaultWindowingWidth_);
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
447 }
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 switch (data_.imageInformation_.GetPhotometricInterpretation())
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
450 {
1634
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
451 case Orthanc::PhotometricInterpretation_Monochrome1:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
452 texture->SetInverted(true);
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
453 break;
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
454
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
455 case Orthanc::PhotometricInterpretation_Monochrome2:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
456 texture->SetInverted(false);
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
457 break;
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
458
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
459 default:
a4418a489e86 improving robustness of DicomInstanceParameters
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1598
diff changeset
460 break;
1206
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
461 }
c93a6218f0cd Fixed photometric interpretation in texture creation
Benjamin Golinvaux <bgo@osimis.io>
parents: 1141
diff changeset
462
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
463 return texture.release();
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
464 }
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
465 }
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
466
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
467
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
468 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
469 (const Orthanc::ImageAccessor& pixelData) const
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
470 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
471 std::unique_ptr<FloatTextureSceneLayer> texture;
768
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 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
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 return new LookupTableTextureSceneLayer(pixelData);
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
476 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
477 else
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
478 {
1298
8a0a62189f46 replacing std::auto_ptr by std::unique_ptr
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1291
diff changeset
479 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
768
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
480 return new LookupTableTextureSceneLayer(*converted);
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
481 }
55411e7da2f7 LookupTableTextureSceneLayer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 762
diff changeset
482 }
980
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
483
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 unsigned int DicomInstanceParameters::GetIndexInSeries() const
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 if (data_.hasIndexInSeries_)
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 return data_.indexInSeries_;
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 else
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
492 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
493 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_";
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
494 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
495 }
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 956
diff changeset
496 }
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
497
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
498
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
499 double DicomInstanceParameters::ApplyRescale(double value) const
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
500 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
501 double factor = data_.doseGridScaling_;
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
502 double offset = 0.0;
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
503
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
504 if (data_.hasRescale_)
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
505 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
506 factor *= data_.rescaleSlope_;
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
507 offset = data_.rescaleIntercept_;
1159
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
508 }
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
509
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
510 return (value * factor + offset);
acb399643945 DicomInstanceParameters::ApplyRescale()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1141
diff changeset
511 }
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
512
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
513
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
514 bool DicomInstanceParameters::ComputeRegularSpacing(double& spacing) const
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
515 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
516 if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE
1161
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 return false;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
519 }
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
520 else if (data_.frameOffsets_.size() == 1)
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
521 {
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
522 spacing = 1; // Edge case: RT-DOSE with one single frame
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
523 return true;
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 else
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
526 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
527 assert(data_.frameOffsets_.size() == GetNumberOfFrames());
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
528
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
529 spacing = std::abs(data_.frameOffsets_[1] - data_.frameOffsets_[0]);
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
530
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
531 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
532 {
1636
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1635
diff changeset
533 double s = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i];
1161
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
534 if (!LinearAlgebra::IsNear(spacing, s, 0.001))
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 false;
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 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
539
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
540 return true;
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
541 }
19b1c8caade4 fix sagittal geometry
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1159
diff changeset
542 }
746
d716bfb3e07c reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
543 }