Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/07/07 16:37:40 $
- Version: $Revision: 1.249 $
+ Date: $Date: 2005/07/24 02:10:48 $
+ Version: $Revision: 1.262 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
// as the Z coordinate,
// 0. for all the coordinates if nothing is found
//
+// Image Position (Patient) (0020,0032) VM=3 What is it used for?
+// -->
+// The attribute Patient Orientation (0020,0020) from the General Image Module
+// is of type 2C and has the condition Required if image does not require
+// Image Orientation (0020,0037) and Image Position (0020,0032).
+// However, if the image does require the attributes
+// - Image Orientation (Patient) (0020,0037), VM=6
+// - Image Position Patient (0020,0032), VM=3
+// then attribute Patient Orientation (0020,0020) should not be present
+// in the images.
+//
+// Remember also :
+// Patient Position (0018,5100) values : HFP = Head First-Prone
+// HFS = Head First-Supine
+// HFDR = Head First-Decubitus Right
+// HFDL = Head First-Decubitus Left
+// FFDR = Feet First-Decubitus Right
+// FFDL = Feet First-Decubitus Left
+// FFP = Feet First-Prone
+// FFS = Feet First-Supine
+// can also find SEMIERECT
+// SUPINE
+// CS 2 Patient Orientation (0020 0020)
+// When the coordinates of the image
+// are always present, this field is almost never used.
+// Better we don't tust it too much ...
+// Found Values are : L\P
+// L\FP
+// P\F
+// L\F
+// P\FR
+// R\F
+//
+// (0020|0037) [Image Orientation (Patient)] [1\0\0\0\1\0 ]
+
+
// ---------------------------------------------------------------
//
#include "gdcmFile.h"
#include <vector>
#include <stdio.h> //sscanf
#include <stdlib.h> // for atoi
+#include <math.h> // for pow
namespace gdcm
{
+
//-----------------------------------------------------------------------------
// Constructor / Destructor
NumPixel = 0x0010;
}
-/**
- * \brief Constructor
- * @param filename name of the file whose header we want to analyze
- */
-File::File( std::string const &filename )
- :Document( )
-{
- RLEInfo = new RLEFramesInfo;
- JPEGInfo = new JPEGFragmentsInfo;
-
- Load( filename ); // gdcm::Document is first Loaded, then the 'File part'
-}
/**
* \brief Canonical destructor.
return DoTheLoadingJob( );
}
-/**
- * \brief Loader. (DEPRECATED : not to break the API)
- * @param fileName file to be open for parsing
- * @return false if file cannot be open or no swap info was found,
- * or no tag was found.
- */
-bool File::Load( std::string const &fileName )
-{
- SetFileName( fileName );
- if ( ! this->Document::Load( ) )
- return false;
-
- return DoTheLoadingJob( );
-}
/**
* \brief Does the Loading Job (internal use only)
* @param iop adress of the (6)float array to receive values
* @return cosines of image orientation patient
*/
-void File::GetImageOrientationPatient( float iop[6] )
+bool File::GetImageOrientationPatient( float iop[6] )
{
std::string strImOriPat;
//iop is supposed to be float[6]
&iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
{
gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
+ return false;
}
}
//For ACR-NEMA
&iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
{
gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
+ return false;
}
}
+ return true;
}
/**
if ( d == NULL)
continue;
- if ( dynamic_cast<BinEntry *>(d)
- || dynamic_cast<SeqEntry *>(d) )
- continue;
+ if ( dynamic_cast<SeqEntry *>(d) )
+ {
+ gdcmWarningMacro( "You cannot 'Anonymize a SeqEntry ");
+ continue;
+ }
offset = d->GetOffset();
lgth = d->GetLength();
/**
* \brief anonymize a File (remove Patient's personal info passed with
* AddAnonymizeElement()
+ * \note You cannot Anonymize a BinEntry (to be fixed)
*/
bool File::AnonymizeFile()
{
if ( d == NULL)
continue;
- if ( dynamic_cast<BinEntry *>(d)
- || dynamic_cast<SeqEntry *>(d) )
+ if ( dynamic_cast<SeqEntry *>(d) )
+ {
+ gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry ");
continue;
+ }
- SetValEntry ((*it).Value, (*it).Group, (*it).Elem);
+ if ( dynamic_cast<BinEntry *>(d) )
+ {
+ gdcmWarningMacro( "To 'Anonymize' a BinEntry, better use AnonymizeNoLoad (FIXME) ");
+ continue;
+ }
+ else
+ SetValEntry ((*it).Value, (*it).Group, (*it).Elem);
}
}
}
}
+// These are the deprecated method that one day should be removed (after the next release)
+
+#ifndef GDCM_LEGACY_REMOVE
+/**
+ * \brief Constructor (DEPRECATED : temporaryly kept not to break the API)
+ * @param filename name of the file whose header we want to analyze
+ * @deprecated do not use any longer
+ */
+File::File( std::string const &filename )
+ :Document( )
+{
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
+
+ SetFileName( filename );
+ Load( ); // gdcm::Document is first Loaded, then the 'File part'
+}
+
+/**
+ * \brief Loader. (DEPRECATED : temporaryly kept not to break the API)
+ * @param fileName file to be open for parsing
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
+ */
+bool File::Load( std::string const &fileName )
+{
+ GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
+ File::Load());
+ SetFileName( fileName );
+ if ( ! this->Document::Load( ) )
+ return false;
+
+ return DoTheLoadingJob( );
+}
+#endif
+
+// -----------------------------------------------------------------------------------------
+// THERALYS Algorithm to determine the most similar basic orientation
+//
+// Transliterated from original Python code.
+// Kept as close as possible to the original code
+// in order to speed up any further modif of Python code :-(
+// ------------------------------------------------------------------------------------------
+
+/**
+ * \brief THERALYS' Algorithm to determine the most similar basic orientation
+ * (Axial, Coronal, Sagital) of the image
+ * \note Should be run on the first gdcm::File of a 'coherent' Serie
+ * @return orientation code
+ * @return orientation code
+ * # 0 : Not Applicable (neither 0020,0037 Image Orientation Patient
+ * # nor 0020,0032Image Position found )
+ * # 1 : Axial
+ * # -1 : Axial invert
+ * # 2 : Coronal
+ * # -2 : Coronal invert
+ * # 3 : Sagital
+ * # -3 : Sagital invert
+ * # 4 : Heart Axial
+ * # -4 : Heart Axial invert
+ * # 5 : Heart Coronal
+ * # -5 : Heart Coronal invert
+ * # 6 : Heart Sagital
+ * # -6 : Heart Sagital invert
+ */
+double File::TypeOrientation( )
+{
+ float iop[6];
+ bool succ = GetImageOrientationPatient( iop );
+ if ( !succ )
+ {
+ return 0.;
+ }
+
+ vector3D ori1;
+ vector3D ori2;
+
+ ori1.x = iop[0]; ori1.y = iop[1]; ori1.z = iop[2];
+ ori1.x = iop[3]; ori2.y = iop[4]; ori2.z = iop[5];
+
+ // two perpendicular vectors describe one plane
+ double dicPlane[6][2][3] =
+ { { {1, 0, 0 },{0, 1, 0 } }, // Axial
+ { {1, 0, 0 },{0, 0, -1 } }, // Coronal
+ { {0, 1, 0 },{0, 0, -1 } }, // Sagittal
+ { { 0.8, 0.5, 0.0 },{-0.1, 0.1 , -0.95 } }, // Axial - HEART
+ { { 0.8, 0.5, 0.0 },{-0.6674, 0.687, 0.1794} }, // Coronal - HEART
+ { {-0.1, 0.1, -0.95},{-0.6674, 0.687, 0.1794} } // Sagittal - HEART
+ };
+
+ vector3D refA;
+ vector3D refB;
+ int i = 0;
+ Res res; // [ <result> , <memory of the last succes calcule> ]
+ res.first = 0;
+ res.second = 99999;
+ for (int numDicPlane=0; numDicPlane<6; numDicPlane++)
+ {
+ ++i;
+ // refA=plane[0]
+ refA.x = dicPlane[numDicPlane][0][0];
+ refA.y = dicPlane[numDicPlane][0][1];
+ refA.z = dicPlane[numDicPlane][0][2];
+ // refB=plane[1]
+ refB.x = dicPlane[numDicPlane][1][0];
+ refB.y = dicPlane[numDicPlane][1][1];
+ refB.z = dicPlane[numDicPlane][1][2];
+ res=VerfCriterion( i, CalculLikelyhood2Vec(refA,refB,ori1,ori2), res );
+ res=VerfCriterion( -i, CalculLikelyhood2Vec(refB,refA,ori1,ori2), res );
+ }
+ return res.first;
+/*
+// i=0
+// res=[0,99999] ## [ <result> , <memory of the last succes calculus> ]
+// for plane in dicPlane:
+// i=i+1
+// refA=plane[0]
+// refB=plane[1]
+// res=self.VerfCriterion( i , self.CalculLikelyhood2Vec(refA,refB,ori1,ori2) , res )
+// res=self.VerfCriterion( -i , self.CalculLikelyhood2Vec(refB,refA,ori1,ori2) , res )
+// return res[0]
+*/
+
+}
+
+Res
+File::VerfCriterion(int typeCriterion, double criterionNew, Res const & in)
+{
+ Res res;
+ double criterion = in.second;
+ if (criterionNew < criterion)
+ {
+ res.first = criterionNew;
+ res.second = typeCriterion;
+ }
+/*
+// type = res[0]
+// criterion = res[1]
+// # if criterionNew<0.1 and criterionNew<criterion:
+// if criterionNew<criterion:
+// criterion=criterionNew
+// type=typeCriterion
+// return [ type , criterion ]
+*/
+ return res;
+}
+
+inline double square_dist(vector3D const &v1, vector3D const & v2)
+{
+ double res;
+ res = (v1.x - v2.x)*(v1.x - v2.x) +
+ (v1.y - v2.y)*(v1.y - v2.y) +
+ (v1.z - v2.z)*(v1.z - v2.z);
+ return res;
+}
+
+//------------------------- Purpose : -----------------------------------
+//- This function determines the orientation similarity of two planes.
+// Each plane is described by two vectors.
+//------------------------- Parameters : --------------------------------
+//- <refA> : - type : vector 3D (double)
+//- <refB> : - type : vector 3D (double)
+// - Description of the first plane
+//- <ori1> : - type : vector 3D (double)
+//- <ori2> : - type : vector 3D (double)
+// - Description of the second plane
+//------------------------- Return : ------------------------------------
+// double : 0 if the planes are perpendicular. While the difference of
+// the orientation between the planes are big more enlarge is
+// the criterion.
+//------------------------- Other : -------------------------------------
+// The calculus is based with vectors normalice
+double
+File::CalculLikelyhood2Vec(vector3D const & refA, vector3D const & refB,
+ vector3D const & ori1, vector3D const & ori2 )
+{
+
+ vector3D ori3 = ProductVectorial(ori1,ori2);
+ vector3D refC = ProductVectorial(refA,refB);
+ double res = square_dist(refC, ori3);
+
+ return sqrt(res);
+}
+
+//------------------------- Purpose : -----------------------------------
+//- Calculus of the poduct vectorial between two vectors 3D
+//------------------------- Parameters : --------------------------------
+//- <vec1> : - type : vector 3D (double)
+//- <vec2> : - type : vector 3D (double)
+//------------------------- Return : ------------------------------------
+// (vec) : - Vector 3D
+//------------------------- Other : -------------------------------------
+vector3D
+File::ProductVectorial(vector3D const & vec1, vector3D const & vec2)
+{
+ vector3D vec3;
+ vec3.x = vec1.y*vec2.z - vec1.z*vec2.y;
+ vec3.y = -( vec1.x*vec2.z - vec1.z*vec2.x);
+ vec3.z = vec1.x*vec2.y - vec1.y*vec2.x;
+
+ return vec3;
+}
+
//-----------------------------------------------------------------------------
// Print
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff