orthanc-stone: OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp annotate

annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1750:5f74ebe2516b

fixed includes

author	Benjamin Golinvaux <bgo@osimis.io>
date	Mon, 22 Feb 2021 14:56:06 +0100
parents	4bedae500652
children	6c246f862b00

rev	line source
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	1 /**
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	2 * Stone of Orthanc
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	4 * Department, University Hospital of Liege, Belgium
1739 9ac2a65d4172 upgrade to year 2021 Sebastien Jodogne <s.jodogne@gmail.com> parents: 1679 diff changeset	5 * Copyright (C) 2017-2021 Osimis S.A., Belgium
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	6 *
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	7 * This program is free software: you can redistribute it and/or
1598 8563ea5d8ae4 relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20 Sebastien Jodogne <s.jodogne@gmail.com> parents: 1596 diff changeset	8 * modify it under the terms of the GNU Lesser General Public License
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	9 * as published by the Free Software Foundation, either version 3 of
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	10 * the License, or (at your option) any later version.
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	11 *
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	12 * This program is distributed in the hope that it will be useful, but
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	13 * WITHOUT ANY WARRANTY; without even the implied warranty of
1598 8563ea5d8ae4 relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20 Sebastien Jodogne <s.jodogne@gmail.com> parents: 1596 diff changeset	14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
8563ea5d8ae4 relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20 Sebastien Jodogne <s.jodogne@gmail.com> parents: 1596 diff changeset	15 * Lesser General Public License for more details.
1596 4fb8fdf03314 removed annoying whitespace Sebastien Jodogne <s.jodogne@gmail.com> parents: 1571 diff changeset	16 *
1598 8563ea5d8ae4 relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20 Sebastien Jodogne <s.jodogne@gmail.com> parents: 1596 diff changeset	17 * You should have received a copy of the GNU Lesser General Public
8563ea5d8ae4 relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20 Sebastien Jodogne <s.jodogne@gmail.com> parents: 1596 diff changeset	18 * License along with this program. If not, see
8563ea5d8ae4 relicensing some files, cf. osimis bm26 and chu agreement on 2020-05-20 Sebastien Jodogne <s.jodogne@gmail.com> parents: 1596 diff changeset	19 * <http://www.gnu.org/licenses/>.
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	20 **/
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	21
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	22
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	23 #include "DicomInstanceParameters.h"
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	24
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	25 #include "../Scene2D/ColorTextureSceneLayer.h"
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	26 #include "../Scene2D/FloatTextureSceneLayer.h"
1750 5f74ebe2516b fixed includes Benjamin Golinvaux <bgo@osimis.io> parents: 1746 diff changeset	27 #include "GeometryToolbox.h"
5f74ebe2516b fixed includes Benjamin Golinvaux <bgo@osimis.io> parents: 1746 diff changeset	28 #include "ImageToolbox.h"
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	29
1455 30deba7bc8e2 simplifying include_directories Sebastien Jodogne <s.jodogne@gmail.com> parents: 1353 diff changeset	30 #include <Images/Image.h>
30deba7bc8e2 simplifying include_directories Sebastien Jodogne <s.jodogne@gmail.com> parents: 1353 diff changeset	31 #include <Images/ImageProcessing.h>
30deba7bc8e2 simplifying include_directories Sebastien Jodogne <s.jodogne@gmail.com> parents: 1353 diff changeset	32 #include <Logging.h>
30deba7bc8e2 simplifying include_directories Sebastien Jodogne <s.jodogne@gmail.com> parents: 1353 diff changeset	33 #include <OrthancException.h>
30deba7bc8e2 simplifying include_directories Sebastien Jodogne <s.jodogne@gmail.com> parents: 1353 diff changeset	34 #include <Toolbox.h>
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	35
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	36
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	37 namespace OrthancStone
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	38 {
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	39 static void ExtractFrameOffsets(Vector& target,
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	40 const Orthanc::DicomMap& dicom,
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	41 unsigned int numberOfFrames)
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	42 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	43 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	44
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	45 std::string increment;
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	46
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	47 if (dicom.LookupStringValue(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false))
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	48 {
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	49 Orthanc::Toolbox::ToUpperCase(increment);
1635 1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	50
1746 4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	51 // We only support volumes where the FrameIncrementPointer (0028,0009) (required) contains
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	52 // the "Grid Frame Offset Vector" tag (DICOM_TAG_GRID_FRAME_OFFSET_VECTOR)
1635 1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	53 if (increment != "3004,000C")
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	54 {
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	55 LOG(WARNING) << "Bad value for the FrameIncrementPointer tags in a multiframe image";
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	56 target.resize(0);
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	57 return;
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	58 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	59 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	60
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	61 if (!LinearAlgebra::ParseVector(target, dicom, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR) \|\|
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	62 target.size() != numberOfFrames)
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	63 {
1746 4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	64 LOG(ERROR) << "The frame offset information (GridFrameOffsetVector (3004,000C)) is missing in a multiframe image";
1635 1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	65
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	66 // DO NOT use ".clear()" here, as the "Vector" class doesn't behave like std::vector!
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	67 target.resize(0);
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	68 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	69 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	70
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	71
1642 5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	72 DicomInstanceParameters::Data::Data(const Orthanc::DicomMap& dicom)
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	73 {
994 1f74bc3459ba fix build due to rename in Orthanc::DicomMap Sebastien Jodogne <s.jodogne@gmail.com> parents: 980 diff changeset	74 if (!dicom.LookupStringValue(studyInstanceUid_, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) \|\|
1f74bc3459ba fix build due to rename in Orthanc::DicomMap Sebastien Jodogne <s.jodogne@gmail.com> parents: 980 diff changeset	75 !dicom.LookupStringValue(seriesInstanceUid_, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false) \|\|
1f74bc3459ba fix build due to rename in Orthanc::DicomMap Sebastien Jodogne <s.jodogne@gmail.com> parents: 980 diff changeset	76 !dicom.LookupStringValue(sopInstanceUid_, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false))
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	77 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	78 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	79 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	80
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	81 std::string s;
1635 1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	82 if (dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false))
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	83 {
1635 1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	84 sopClassUid_ = StringToSopClassUid(s);
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	85 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	86 else
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	87 {
1635 1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	88 sopClassUid_ = SopClassUid_Other;
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	89 }
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	90
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	91 uint32_t n;
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	92 if (dicom.ParseUnsignedInteger32(n, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	93 {
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	94 numberOfFrames_ = n;
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	95 }
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	96 else
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	97 {
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	98 numberOfFrames_ = 1;
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	99 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	100
1635 1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	101 if (!dicom.HasTag(Orthanc::DICOM_TAG_COLUMNS) \|\|
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	102 !dicom.GetValue(Orthanc::DICOM_TAG_COLUMNS).ParseFirstUnsignedInteger(width_))
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	103 {
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	104 width_ = 0;
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	105 }
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	106
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	107 if (!dicom.HasTag(Orthanc::DICOM_TAG_ROWS) \|\|
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	108 !dicom.GetValue(Orthanc::DICOM_TAG_ROWS).ParseFirstUnsignedInteger(height_))
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	109 {
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	110 height_ = 0;
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	111 }
1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	112
1746 4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	113
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	114 bool sliceThicknessPresent = true;
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	115 if (!dicom.ParseDouble(sliceThickness_, Orthanc::DICOM_TAG_SLICE_THICKNESS))
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	116 {
1746 4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	117 LOG(INFO) << "The (non-madatory) slice thickness information is missing in a multiframe image";
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	118 sliceThickness_ = 100.0 * std::numeric_limits<double>::epsilon();
1746 4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	119 sliceThicknessPresent = false;
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	120 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	121
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	122 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dicom);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	123
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	124 std::string position, orientation;
994 1f74bc3459ba fix build due to rename in Orthanc::DicomMap Sebastien Jodogne <s.jodogne@gmail.com> parents: 980 diff changeset	125 if (dicom.LookupStringValue(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
1f74bc3459ba fix build due to rename in Orthanc::DicomMap Sebastien Jodogne <s.jodogne@gmail.com> parents: 980 diff changeset	126 dicom.LookupStringValue(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	127 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	128 geometry_ = CoordinateSystem3D(position, orientation);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	129 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	130
1635 1a714e21ea7c start refactoring DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1634 diff changeset	131 // Must be AFTER setting "numberOfFrames_"
1639 5cdc5b98f14d cppcheck Sebastien Jodogne <s.jodogne@gmail.com> parents: 1637 diff changeset	132 if (numberOfFrames_ > 1)
5cdc5b98f14d cppcheck Sebastien Jodogne <s.jodogne@gmail.com> parents: 1637 diff changeset	133 {
5cdc5b98f14d cppcheck Sebastien Jodogne <s.jodogne@gmail.com> parents: 1637 diff changeset	134 ExtractFrameOffsets(frameOffsets_, dicom, numberOfFrames_);
1746 4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	135
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	136 // if the slice thickness is unknown, we try to infer it from the sequence of grid frame offsets
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	137 // this only works if:
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	138 // - the first offset is 0.0 (case (a) of http://dicom.nema.org/medical/Dicom/2017c/output/chtml/part03/sect_C.8.8.3.2.html)
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	139 // - the offsets are all equal, to some small tolerance
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	140 // - the offsets is positive (increasing throughout the frames)
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	141 if (!sliceThicknessPresent)
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	142 {
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	143 if (frameOffsets_.size() >= 2)
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	144 {
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	145 double sliceThickness = frameOffsets_[1] - frameOffsets_[0];
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	146 bool sameSized = true;
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	147 if (sliceThickness > 0)
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	148 {
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	149 for (size_t i = 2; i < frameOffsets_.size(); ++i)
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	150 {
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	151 double currentThickness = frameOffsets_[i] - frameOffsets_[i-1];
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	152 if (!LinearAlgebra::IsNear(sliceThickness, currentThickness))
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	153 {
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	154 LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: varying spacing)";
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	155 sameSized = false;
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	156 break;
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	157 }
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	158 }
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	159 if (sameSized)
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	160 {
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	161 sliceThickness_ = sliceThickness;
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	162 LOG(INFO) << "SliceThickness was not specified in the Dicom but was inferred from GridFrameOffsetVector (3004,000C).";
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	163 }
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	164 }
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	165 }
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	166 else
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	167 {
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	168 LOG(ERROR) << "Unable to extract slice thickness from GridFrameOffsetVector (3004,000C) (reason: GridFrameOffsetVector not present or too small)";
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	169 }
4bedae500652 Automatically compute SliceThickness from Benjamin Golinvaux <bgo@osimis.io> parents: 1739 diff changeset	170 }
1639 5cdc5b98f14d cppcheck Sebastien Jodogne <s.jodogne@gmail.com> parents: 1637 diff changeset	171 }
5cdc5b98f14d cppcheck Sebastien Jodogne <s.jodogne@gmail.com> parents: 1637 diff changeset	172 else
5cdc5b98f14d cppcheck Sebastien Jodogne <s.jodogne@gmail.com> parents: 1637 diff changeset	173 {
5cdc5b98f14d cppcheck Sebastien Jodogne <s.jodogne@gmail.com> parents: 1637 diff changeset	174 frameOffsets_.resize(0);
5cdc5b98f14d cppcheck Sebastien Jodogne <s.jodogne@gmail.com> parents: 1637 diff changeset	175 }
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	176
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	177 if (sopClassUid_ == SopClassUid_RTDose)
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	178 {
1091 5a18e6a395bc Added DoseUnit tag retrieval to DicomInstanceParameters Benjamin Golinvaux <bgo@osimis.io> parents: 1027 diff changeset	179 static const Orthanc::DicomTag DICOM_TAG_DOSE_UNITS(0x3004, 0x0002);
5a18e6a395bc Added DoseUnit tag retrieval to DicomInstanceParameters Benjamin Golinvaux <bgo@osimis.io> parents: 1027 diff changeset	180
5a18e6a395bc Added DoseUnit tag retrieval to DicomInstanceParameters Benjamin Golinvaux <bgo@osimis.io> parents: 1027 diff changeset	181 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	182 {
1141 7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	183 LOG(ERROR) << "Tag DoseUnits (0x3004, 0x0002) is missing in " << sopInstanceUid_;
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	184 doseUnits_.clear();
1091 5a18e6a395bc Added DoseUnit tag retrieval to DicomInstanceParameters Benjamin Golinvaux <bgo@osimis.io> parents: 1027 diff changeset	185 }
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	186 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	187
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	188 if (dicom.ParseDouble(rescaleIntercept_, Orthanc::DICOM_TAG_RESCALE_INTERCEPT) &&
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	189 dicom.ParseDouble(rescaleSlope_, Orthanc::DICOM_TAG_RESCALE_SLOPE))
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	190 {
1141 7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	191 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	192 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	193 LOG(INFO) << "DOSE HAS Rescale*: rescaleIntercept_ = " << rescaleIntercept_ << " rescaleSlope_ = " << rescaleSlope_;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	194 // WE SHOULD NOT TAKE THE RESCALE VALUE INTO ACCOUNT IN THE CASE OF DOSES
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	195 hasRescale_ = false;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	196 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	197 else
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	198 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	199 hasRescale_ = true;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	200 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	201
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	202 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	203 else
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	204 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	205 hasRescale_ = false;
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	206 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	207
1141 7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	208 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	209 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	210 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	211 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	212 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	213 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	214 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	215 else
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	216 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	217 doseGridScaling_ = 1.0;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	218 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	219 {
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	220 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	221 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	222 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	223
1677 51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	224 bool ok = false;
51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	225
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	226 if (LinearAlgebra::ParseVector(windowingPresetCenters_, dicom, Orthanc::DICOM_TAG_WINDOW_CENTER) &&
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	227 LinearAlgebra::ParseVector(windowingPresetWidths_, dicom, Orthanc::DICOM_TAG_WINDOW_WIDTH))
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	228 {
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	229 if (windowingPresetCenters_.size() == windowingPresetWidths_.size())
1677 51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	230 {
51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	231 ok = true;
51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	232 }
51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	233 else
51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	234 {
51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	235 LOG(ERROR) << "Mismatch in the number of preset windowing widths/centers, ignoring this";
51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	236 ok = false;
51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	237 }
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	238 }
1677 51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	239
51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	240 if (!ok)
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	241 {
1677 51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	242 // Don't use "Vector::clear()", as it has not the same meaning as "std::vector::clear()"
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	243 windowingPresetCenters_.resize(0);
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	244 windowingPresetWidths_.resize(0);
1677 51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	245 }
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	246
980 8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	247 // This computes the "IndexInSeries" metadata from Orthanc (check
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	248 // out "Orthanc::ServerIndex::Store()")
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	249 hasIndexInSeries_ = (
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	250 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_INSTANCE_NUMBER) \|\|
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	251 dicom.ParseUnsignedInteger32(indexInSeries_, Orthanc::DICOM_TAG_IMAGE_INDEX));
1646 4e14735e98f8 preparing to remove FrameExtent Sebastien Jodogne <s.jodogne@gmail.com> parents: 1642 diff changeset	252
4e14735e98f8 preparing to remove FrameExtent Sebastien Jodogne <s.jodogne@gmail.com> parents: 1642 diff changeset	253 if (!dicom.LookupStringValue(
4e14735e98f8 preparing to remove FrameExtent Sebastien Jodogne <s.jodogne@gmail.com> parents: 1642 diff changeset	254 frameOfReferenceUid_, Orthanc::DICOM_TAG_FRAME_OF_REFERENCE_UID, false))
4e14735e98f8 preparing to remove FrameExtent Sebastien Jodogne <s.jodogne@gmail.com> parents: 1642 diff changeset	255 {
4e14735e98f8 preparing to remove FrameExtent Sebastien Jodogne <s.jodogne@gmail.com> parents: 1642 diff changeset	256 frameOfReferenceUid_.clear();
4e14735e98f8 preparing to remove FrameExtent Sebastien Jodogne <s.jodogne@gmail.com> parents: 1642 diff changeset	257 }
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	258 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	259
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	260
1642 5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	261 const Orthanc::DicomImageInformation& DicomInstanceParameters::GetImageInformation() const
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	262 {
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	263 assert(tags_.get() != NULL);
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	264
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	265 if (imageInformation_.get() == NULL)
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	266 {
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	267 const_cast<DicomInstanceParameters&>(*this).imageInformation_.
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	268 reset(new Orthanc::DicomImageInformation(GetTags()));
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	269
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	270 assert(imageInformation_->GetWidth() == GetWidth());
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	271 assert(imageInformation_->GetHeight() == GetHeight());
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	272 assert(imageInformation_->GetNumberOfFrames() == GetNumberOfFrames());
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	273 }
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	274
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	275 assert(imageInformation_.get() != NULL);
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	276 return *imageInformation_;
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	277 }
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	278
5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	279
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	280 CoordinateSystem3D DicomInstanceParameters::GetFrameGeometry(unsigned int frame) const
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	281 {
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	282 if (frame >= data_.numberOfFrames_)
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	283 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	284 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	285 }
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	286 else if (data_.frameOffsets_.empty())
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	287 {
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	288 return data_.geometry_;
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	289 }
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	290 else
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	291 {
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	292 assert(data_.frameOffsets_.size() == data_.numberOfFrames_);
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	293
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	294 return CoordinateSystem3D(
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	295 data_.geometry_.GetOrigin() + data_.frameOffsets_[frame] * data_.geometry_.GetNormal(),
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	296 data_.geometry_.GetAxisX(),
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	297 data_.geometry_.GetAxisY());
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	298 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	299 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	300
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	301
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	302 bool DicomInstanceParameters::IsPlaneWithinSlice(unsigned int frame,
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	303 const CoordinateSystem3D& plane) const
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	304 {
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	305 if (frame >= data_.numberOfFrames_)
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	306 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	307 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	308 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	309
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	310 CoordinateSystem3D tmp = data_.geometry_;
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	311
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	312 if (frame != 0)
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	313 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	314 tmp = GetFrameGeometry(frame);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	315 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	316
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	317 double distance;
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	318
757 f7c236894c1a cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 746 diff changeset	319 return (CoordinateSystem3D::ComputeDistance(distance, tmp, plane) &&
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	320 distance <= data_.sliceThickness_ / 2.0);
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	321 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	322
1637 d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	323
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	324 bool DicomInstanceParameters::IsColor() const
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	325 {
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	326 Orthanc::PhotometricInterpretation photometric =
1642 5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	327 GetImageInformation().GetPhotometricInterpretation();
1637 d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	328
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	329 return (photometric != Orthanc::PhotometricInterpretation_Monochrome1 &&
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	330 photometric != Orthanc::PhotometricInterpretation_Monochrome2);
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	331 }
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	332
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	333
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	334 void DicomInstanceParameters::ApplyRescaleAndDoseScaling(Orthanc::ImageAccessor& image,
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	335 bool useDouble) const
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	336 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	337 if (image.GetFormat() != Orthanc::PixelFormat_Float32)
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	338 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	339 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	340 }
1141 7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	341
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	342 double factor = data_.doseGridScaling_;
1141 7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	343 double offset = 0.0;
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	344
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	345 if (data_.hasRescale_)
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	346 {
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	347 factor *= data_.rescaleSlope_;
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	348 offset = data_.rescaleIntercept_;
1141 7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	349 }
7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	350
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	351 if (!LinearAlgebra::IsNear(factor, 1) \|\|
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	352 !LinearAlgebra::IsNear(offset, 0))
1141 7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	353 {
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	354 const unsigned int width = image.GetWidth();
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	355 const unsigned int height = image.GetHeight();
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	356
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	357 for (unsigned int y = 0; y < height; y++)
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	358 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	359 float* p = reinterpret_cast<float*>(image.GetRow(y));
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	360
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	361 if (useDouble)
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	362 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	363 // Slower, accurate implementation using double
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	364 for (unsigned int x = 0; x < width; x++, p++)
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	365 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	366 double value = static_cast<double>(*p);
1141 7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	367 p = static_cast<float>(value factor + offset);
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	368 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	369 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	370 else
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	371 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	372 // Fast, approximate implementation using float
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	373 for (unsigned int x = 0; x < width; x++, p++)
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	374 {
1141 7681f3943748 Changed handling of DoseGridScaling: before this commit, rescaleSlope was set to Benjamin Golinvaux <bgo@osimis.io> parents: 1091 diff changeset	375 p = (p) * static_cast<float>(factor) + static_cast<float>(offset);
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	376 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	377 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	378 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	379 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	380 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	381
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	382 double DicomInstanceParameters::GetRescaleIntercept() const
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	383 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	384 if (data_.hasRescale_)
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	385 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	386 return data_.rescaleIntercept_;
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	387 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	388 else
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	389 {
956 a7351ad54960 Made IsContextLost automatically set the flag by checking with the emscripten Benjamin Golinvaux <bgo@osimis.io> parents: 949 diff changeset	390 LOG(ERROR) << "DicomInstanceParameters::GetRescaleIntercept(): !data_.hasRescale_";
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	391 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	392 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	393 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	394
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	395
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	396 double DicomInstanceParameters::GetRescaleSlope() const
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	397 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	398 if (data_.hasRescale_)
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	399 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	400 return data_.rescaleSlope_;
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	401 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	402 else
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	403 {
956 a7351ad54960 Made IsContextLost automatically set the flag by checking with the emscripten Benjamin Golinvaux <bgo@osimis.io> parents: 949 diff changeset	404 LOG(ERROR) << "DicomInstanceParameters::GetRescaleSlope(): !data_.hasRescale_";
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	405 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	406 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	407 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	408
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	409
1637 d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	410 Orthanc::PixelFormat DicomInstanceParameters::GetExpectedPixelFormat() const
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	411 {
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	412 if (GetSopClassUid() == SopClassUid_RTDose)
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	413 {
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	414 switch (GetImageInformation().GetBitsStored())
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	415 {
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	416 case 16:
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	417 return Orthanc::PixelFormat_Grayscale16;
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	418
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	419 case 32:
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	420 return Orthanc::PixelFormat_Grayscale32;
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	421
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	422 default:
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	423 return Orthanc::PixelFormat_Grayscale16; // Rough guess
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	424 }
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	425 }
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	426 else if (IsColor())
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	427 {
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	428 return Orthanc::PixelFormat_RGB24;
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	429 }
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	430 else if (GetImageInformation().IsSigned())
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	431 {
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	432 return Orthanc::PixelFormat_SignedGrayscale16;
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	433 }
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	434 else
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	435 {
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	436 return Orthanc::PixelFormat_Grayscale16; // Rough guess
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	437 }
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	438 }
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	439
d569effcd433 cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1636 diff changeset	440
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	441 size_t DicomInstanceParameters::GetWindowingPresetsCount() const
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	442 {
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	443 assert(data_.windowingPresetCenters_.size() == data_.windowingPresetWidths_.size());
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	444 return data_.windowingPresetCenters_.size();
1677 51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	445 }
51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	446
51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	447
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	448 float DicomInstanceParameters::GetWindowingPresetCenter(size_t i) const
1677 51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	449 {
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	450 if (i < GetWindowingPresetsCount())
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	451 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	452 return static_cast<float>(data_.windowingPresetCenters_[i]);
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	453 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	454 else
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	455 {
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	456 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	457 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	458 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	459
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	460
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	461 float DicomInstanceParameters::GetWindowingPresetWidth(size_t i) const
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	462 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	463 if (i < GetWindowingPresetsCount())
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	464 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	465 return static_cast<float>(data_.windowingPresetWidths_[i]);
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	466 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	467 else
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	468 {
1677 51bab5188a13 start multiple preset windowings Sebastien Jodogne <s.jodogne@gmail.com> parents: 1646 diff changeset	469 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	470 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	471 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	472
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	473
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	474 static void GetWindowingBounds(float& low,
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	475 float& high,
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	476 double center, // in
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	477 double width) // in
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	478 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	479 low = static_cast<float>(center - width / 2.0);
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	480 high = static_cast<float>(center + width / 2.0);
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	481 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	482
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	483
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	484 void DicomInstanceParameters::GetWindowingPresetsUnion(float& center,
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	485 float& width) const
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	486 {
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	487 assert(tags_.get() != NULL);
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	488 size_t s = GetWindowingPresetsCount();
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	489
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	490 if (s > 0)
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	491 {
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	492 // Use the largest windowing given all the preset windowings
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	493 // that are available in the DICOM tags
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	494 float low, high;
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	495 GetWindowingBounds(low, high, GetWindowingPresetCenter(0), GetWindowingPresetWidth(0));
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	496
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	497 for (size_t i = 1; i < s; i++)
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	498 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	499 float a, b;
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	500 GetWindowingBounds(a, b, GetWindowingPresetCenter(i), GetWindowingPresetWidth(i));
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	501 low = std::min(low, a);
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	502 high = std::max(high, b);
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	503 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	504
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	505 assert(low <= high);
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	506
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	507 if (LinearAlgebra::IsNear(low, high))
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	508 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	509 // Cannot infer a suitable windowing from the available tags
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	510 center = 128.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	511 width = 256.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	512 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	513 else
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	514 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	515 center = (low + high) / 2.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	516 width = (high - low);
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	517 }
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	518 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	519 else
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	520 {
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	521 float a, b;
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	522 if (tags_->ParseFloat(a, Orthanc::DICOM_TAG_SMALLEST_IMAGE_PIXEL_VALUE) &&
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	523 tags_->ParseFloat(b, Orthanc::DICOM_TAG_LARGEST_IMAGE_PIXEL_VALUE) &&
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	524 a < b)
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	525 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	526 center = (a + b) / 2.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	527 width = (b - a);
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	528 }
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	529 else
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	530 {
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	531 // Cannot infer a suitable windowing from the available tags
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	532 center = 128.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	533 width = 256.0f;
5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	534 }
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	535 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	536 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	537
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	538
768 55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	539 Orthanc::ImageAccessor* DicomInstanceParameters::ConvertToFloat(const Orthanc::ImageAccessor& pixelData) const
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	540 {
1298 8a0a62189f46 replacing std::auto_ptr by std::unique_ptr Sebastien Jodogne <s.jodogne@gmail.com> parents: 1291 diff changeset	541 std::unique_ptr<Orthanc::Image> converted(new Orthanc::Image(Orthanc::PixelFormat_Float32,
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	542 pixelData.GetWidth(),
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	543 pixelData.GetHeight(),
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	544 false));
768 55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	545 Orthanc::ImageProcessing::Convert(*converted, pixelData);
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	546
1287 8e82fdc6200e Heavy (temporary) logging in the path that leads Benjamin Golinvaux <bgo@osimis.io> parents: 1270 diff changeset	547
768 55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	548 // Correct rescale slope/intercept if need be
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	549 //ApplyRescaleAndDoseScaling(*converted, (pixelData.GetFormat() == Orthanc::PixelFormat_Grayscale32));
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	550 ApplyRescaleAndDoseScaling(*converted, false);
768 55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	551
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	552 return converted.release();
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	553 }
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	554
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	555
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	556 TextureBaseSceneLayer* DicomInstanceParameters::CreateTexture
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	557 (const Orthanc::ImageAccessor& pixelData) const
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	558 {
1353 af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	559 // {
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	560 // const Orthanc::ImageAccessor& source = pixelData;
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	561 // const void* sourceBuffer = source.GetConstBuffer();
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	562 // intptr_t sourceBufferInt = reinterpret_cast<intptr_t>(sourceBuffer);
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	563 // int sourceWidth = source.GetWidth();
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	564 // int sourceHeight = source.GetHeight();
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	565 // int sourcePitch = source.GetPitch();
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	566
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	567 // // TODO: turn error into trace below
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	568 // LOG(ERROR) << "ConvertGrayscaleToFloat \| source:"
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	569 // << " W = " << sourceWidth << " H = " << sourceHeight
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	570 // << " P = " << sourcePitch << " B = " << sourceBufferInt
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	571 // << " B % 4 == " << sourceBufferInt % 4;
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	572 // }
af65bce18951 Dummy commented debug block Benjamin Golinvaux <bgo@osimis.io> parents: 1300 diff changeset	573
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	574 assert(sizeof(float) == 4);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	575
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	576 Orthanc::PixelFormat sourceFormat = pixelData.GetFormat();
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	577
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	578 if (sourceFormat != GetExpectedPixelFormat())
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	579 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	580 throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	581 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	582
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	583 if (sourceFormat == Orthanc::PixelFormat_RGB24)
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	584 {
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	585 // 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	586 return new ColorTextureSceneLayer(pixelData);
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	587 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	588 else
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	589 {
768 55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	590 // 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	591 std::unique_ptr<FloatTextureSceneLayer> texture;
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	592
768 55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	593 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	594 {
768 55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	595 texture.reset(new FloatTextureSceneLayer(pixelData));
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	596 }
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	597 else
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	598 {
1298 8a0a62189f46 replacing std::auto_ptr by std::unique_ptr Sebastien Jodogne <s.jodogne@gmail.com> parents: 1291 diff changeset	599 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	600 texture.reset(new FloatTextureSceneLayer(*converted));
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	601 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	602
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	603 if (GetWindowingPresetsCount() > 0)
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	604 {
1679 5b8b88e5bfd6 successfully running unit tests in WebAssembly Sebastien Jodogne <s.jodogne@gmail.com> parents: 1677 diff changeset	605 texture->SetCustomWindowing(GetWindowingPresetCenter(0), GetWindowingPresetWidth(0));
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	606 }
1206 c93a6218f0cd Fixed photometric interpretation in texture creation Benjamin Golinvaux <bgo@osimis.io> parents: 1141 diff changeset	607
1642 5cc589bfb385 lazy computation of DicomInstanceParameters::GetImageInformation() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1639 diff changeset	608 switch (GetImageInformation().GetPhotometricInterpretation())
1206 c93a6218f0cd Fixed photometric interpretation in texture creation Benjamin Golinvaux <bgo@osimis.io> parents: 1141 diff changeset	609 {
1634 a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	610 case Orthanc::PhotometricInterpretation_Monochrome1:
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	611 texture->SetInverted(true);
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	612 break;
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	613
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	614 case Orthanc::PhotometricInterpretation_Monochrome2:
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	615 texture->SetInverted(false);
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	616 break;
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	617
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	618 default:
a4418a489e86 improving robustness of DicomInstanceParameters Sebastien Jodogne <s.jodogne@gmail.com> parents: 1598 diff changeset	619 break;
1206 c93a6218f0cd Fixed photometric interpretation in texture creation Benjamin Golinvaux <bgo@osimis.io> parents: 1141 diff changeset	620 }
c93a6218f0cd Fixed photometric interpretation in texture creation Benjamin Golinvaux <bgo@osimis.io> parents: 1141 diff changeset	621
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	622 return texture.release();
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	623 }
d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	624 }
768 55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	625
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	626
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	627 LookupTableTextureSceneLayer* DicomInstanceParameters::CreateLookupTableTexture
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	628 (const Orthanc::ImageAccessor& pixelData) const
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	629 {
1298 8a0a62189f46 replacing std::auto_ptr by std::unique_ptr Sebastien Jodogne <s.jodogne@gmail.com> parents: 1291 diff changeset	630 std::unique_ptr<FloatTextureSceneLayer> texture;
768 55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	631
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	632 if (pixelData.GetFormat() == Orthanc::PixelFormat_Float32)
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	633 {
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	634 return new LookupTableTextureSceneLayer(pixelData);
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	635 }
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	636 else
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	637 {
1298 8a0a62189f46 replacing std::auto_ptr by std::unique_ptr Sebastien Jodogne <s.jodogne@gmail.com> parents: 1291 diff changeset	638 std::unique_ptr<Orthanc::ImageAccessor> converted(ConvertToFloat(pixelData));
768 55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	639 return new LookupTableTextureSceneLayer(*converted);
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	640 }
55411e7da2f7 LookupTableTextureSceneLayer Sebastien Jodogne <s.jodogne@gmail.com> parents: 762 diff changeset	641 }
980 8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	642
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	643
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	644 unsigned int DicomInstanceParameters::GetIndexInSeries() const
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	645 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	646 if (data_.hasIndexInSeries_)
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	647 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	648 return data_.indexInSeries_;
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	649 }
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	650 else
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	651 {
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	652 LOG(ERROR) << "DicomInstanceParameters::GetIndexInSeries(): !data_.hasIndexInSeries_";
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	653 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	654 }
8e497a4e3d96 DicomInstanceParameters::GetIndexInSeries() Sebastien Jodogne <s.jodogne@gmail.com> parents: 956 diff changeset	655 }
1159 acb399643945 DicomInstanceParameters::ApplyRescale() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1141 diff changeset	656
acb399643945 DicomInstanceParameters::ApplyRescale() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1141 diff changeset	657
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	658 double DicomInstanceParameters::ApplyRescale(double value) const
1159 acb399643945 DicomInstanceParameters::ApplyRescale() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1141 diff changeset	659 {
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	660 double factor = data_.doseGridScaling_;
1159 acb399643945 DicomInstanceParameters::ApplyRescale() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1141 diff changeset	661 double offset = 0.0;
acb399643945 DicomInstanceParameters::ApplyRescale() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1141 diff changeset	662
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	663 if (data_.hasRescale_)
1159 acb399643945 DicomInstanceParameters::ApplyRescale() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1141 diff changeset	664 {
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	665 factor *= data_.rescaleSlope_;
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	666 offset = data_.rescaleIntercept_;
1159 acb399643945 DicomInstanceParameters::ApplyRescale() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1141 diff changeset	667 }
acb399643945 DicomInstanceParameters::ApplyRescale() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1141 diff changeset	668
acb399643945 DicomInstanceParameters::ApplyRescale() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1141 diff changeset	669 return (value * factor + offset);
acb399643945 DicomInstanceParameters::ApplyRescale() Sebastien Jodogne <s.jodogne@gmail.com> parents: 1141 diff changeset	670 }
1161 19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	671
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	672
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	673 bool DicomInstanceParameters::ComputeRegularSpacing(double& spacing) const
1161 19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	674 {
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	675 if (data_.frameOffsets_.size() == 0) // Not a RT-DOSE
1161 19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	676 {
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	677 return false;
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	678 }
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	679 else if (data_.frameOffsets_.size() == 1)
1161 19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	680 {
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	681 spacing = 1; // Edge case: RT-DOSE with one single frame
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	682 return true;
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	683 }
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	684 else
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	685 {
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	686 assert(data_.frameOffsets_.size() == GetNumberOfFrames());
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	687
d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	688 spacing = std::abs(data_.frameOffsets_[1] - data_.frameOffsets_[0]);
1161 19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	689
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	690 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	691 {
1636 d1e0b08b809d cont Sebastien Jodogne <s.jodogne@gmail.com> parents: 1635 diff changeset	692 double s = data_.frameOffsets_[i + 1] - data_.frameOffsets_[i];
1161 19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	693 if (!LinearAlgebra::IsNear(spacing, s, 0.001))
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	694 {
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	695 return false;
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	696 }
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	697 }
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	698
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	699 return true;
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	700 }
19b1c8caade4 fix sagittal geometry Sebastien Jodogne <s.jodogne@gmail.com> parents: 1159 diff changeset	701 }
746 d716bfb3e07c reorganization Sebastien Jodogne <s.jodogne@gmail.com> parents: diff changeset	702 }

Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Toolbox/DicomInstanceParameters.cpp @ 1750:5f74ebe2516b