Program: gdcm
Module: $RCSfile: vtkGdcm4DSplitter.cxx,v $
Language: C++
- Date: $Date: 2011/03/29 15:45:38 $
- Version: $Revision: 1.4 $
+ Date: $Date: 2011/04/11 11:28:31 $
+ Version: $Revision: 1.9 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
- User choosen tag
void setSplitOnTag(unsigned short splitGroup, unsigned short splitElem);
void setSplitConvertToFloat(bool conv);
+ - UserDefined Function
+ void setSortOnUserFunction (FoncComp f);
+
+ for 'true' 3D image sets :
+ - if you want to get a single 3D vtkImageData, use SplitOnOrientation -i.e. no split-
+ - if you want to get a vector of 2D vtkImageData, use SplitOnPosition -i.e. one slice in each 'XCoherent filesite'-
+
+ for 'true' 4D multi-orientation image sets (i.e. a stack of axial + sagital + coronal images, at different instants ...)
+ --> this is 5D, right?
+ Nothing done, yet.
+
. Choose 'sort' criterion :
--------------------------
- ImagePositionPatient
- void setSortOnPosition();
- - User choosen tag
- void setSortOnTag(unsigned short sortGroup, unsigned short sortElem);
- void setSortConvertToFloat(bool conv)
-
-. Execute
+ void setSortOnPosition();
+ - ImageOrientationPatient
+ ==> Only in your dreams!
+ ==> or, please, write a IOP sorter ...
+ - UserDefined Function
+ void setSortOnUserFunction (FoncComp f);
+ - File name
+ void setSortOnFileName()
+
+. Execute :
-----------
bool Go();
. Get the result
----------------
- -a single vtkImageData:
- vtkImageData *GetImageData();
+// -a single vtkImageData:
+// vtkImageData *GetImageData();
- a vector of vtkImageData
std::vector<vtkImageData*> *GetImageDataVector();
SortOnPosition(false), SortOnOrientation(false), SortOnTag(false),
SortGroup(0), SortElem(0), SortConvertToFloat(false),
- Recursive(false), TypeDir(0),
- verbose(true)
+ Recursive(false), TypeDir(0),
+ verbose(false)
{
}
std::vector<vtkImageData*> * vtkGdcm4DSplitter::GetImageDataVector()
- {
- if (verbose) std::cout << "TypeDir " << TypeDir << std::endl;
+ {
+/*
+ if (verbose) std::cout << "GetImageDataVector : TypeResult " << TypeResult << std::endl;
if (TypeResult == 2)
return ImageDataVector;
else
}
else
return (std::vector<vtkImageData*>*) NULL;
+*/
+ return ImageDataVector;
}
vtkImageData *vtkGdcm4DSplitter::GetImageData()
{
+ /*
+ if (verbose) std::cout << "GetImageData : TypeResult " << TypeResult << std::endl;
if (TypeResult == 1)
return ImageData;
else
- if (TypeResult == 1)
+ if (TypeResult == 2)
{
return (*ImageDataVector)[0];
}
else
return (vtkImageData*) NULL;
- }
-
+*/
+ return (*ImageDataVector)[0];
+ }
bool vtkGdcm4DSplitter::setDirName(std::string &dirName)
{
bool vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
{
- if (verbose) printf ("%04x %04x\n", this->SortGroup,this->SortElem);
- if (verbose) std :: cout << file1->GetEntryString(SortGroup,SortElem).c_str() << " : "
+ /* if (verbose) printf ("%04x %04x\n", this->SortGroup,this->SortElem);
+ if (verbose) std :: cout << file1->GetEntryString(SortGroup,SortElem).c_str() << " : "
<< atof(file1->GetEntryString(SortGroup,SortElem).c_str())
<< std::endl;
- return atof(file1->GetEntryString(SortGroup,SortElem).c_str()) < atof(file2->GetEntryString(SortGroup,SortElem).c_str());
+*/
+// return atof(file1->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem).c_str()) < atof(file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem).c_str());
+ return atof(file1->GetEntryString(SortGroup,SortElem).c_str()) < atof(file2->GetEntryString(SortGroup,SortElem).c_str());
}
bool vtkGdcm4DSplitter::CompareOnSortTag(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
{
- return file1->GetEntryString(SortGroup,SortElem) < file2->GetEntryString(SortGroup,SortElem);
+ return file1->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem) < file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem);
}
-
+
+
bool vtkGdcm4DSplitter::Go()
{
if (!SplitOnPosition && !SplitOnOrientation && !SplitOnTag )
if (SplitOnOrientation)
{
- s->SetDropDuplicatePositions(false);
- xcm = s->SplitOnOrientation(l);
+ s->SetDropDuplicatePositions(false);
+ xcm = s->SplitOnOrientation(l);
}
else if (SplitOnPosition)
{
- s->SetDropDuplicatePositions(true);
- xcm = s->SplitOnPosition(l);
+ s->SetDropDuplicatePositions(true);
+ xcm = s->SplitOnPosition(l);
+ // reorg the std::map xcm according to position // JPR
+ // the key of xcm follows lexicographical order
+ // (that may be different than the 'distance' order)
+ // we have to reorganize it!
+ reorgXCoherentFileSetmap(xcm);
}
else if (SplitOnTag)
{
if (verbose)
std::cout << "--- xCoherentName = [" << (*i).first << "]" << std::endl;
}
+
// XCoherentFileSetmap map < critère de split, FileList (= std::vector de gdcm::File*) >
for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
else if (SortOnOrientation)
{
if (verbose) std::cout << "SortOnOrientation" << std::endl;
- /// \TODO SortOnOrientation()
- // Within a 'just to see' program,
- // OrderFileList() causes trouble, since some files
- // (eg:MIP views) don't have 'Position', now considered as mandatory
- // --> Activated on user demand.
-
- // Information is in :
- // 0020,0032 : Image Position Patient
- // 0020,0030 : Image Position (RET)
+ /// \TODO SortOnOrientation()
// we still miss an algo to sort an Orientation, given by 6 cosines!
// Anything like this, in GDCM2?
{
if (verbose) std::cout << "SortOnTag" << std::endl;
printf ("--> %04x %04x\n", SortGroup,SortElem);
+ std::cout << "Sorry, troubles not solved yet; use SortOnUserFunction, right now!" << std::endl;
+
+ /* ==> WARNING : This one has troubles; do NOT use it, right now!
+ // a pointer to fonction cannot be casted as a pointer to member function!
+ // Use SortOnUserFunction, instead!
+
if ( SortConvertToFloat )
s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
( &vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat));
// Anything like this, in GDCM2?
s->UserOrdering((*i).second);
- if (verbose) std::cout << "Out of SortOnTag" << std::endl;
+ */
+
+ //if (verbose) std::cout << "Out of SortOnTag" << std::endl;
+ std::cout << "NO ordering performed :-( " << std::endl;
+ }
+
+ else if (SortOnUserFunction)
+ {
+ if (verbose) std::cout << "SortOnUserFunction" << std::endl;
+ s->SetUserLessThanFunction( UserCompareFunction );
+ // Anything like this, in GDCM2?
+ s->UserOrdering((*i).second);
+ if (verbose) std::cout << "Out of SortOnUserFunction" << std::endl;
}
reader->SetCoherentFileList((*i).second);
reader->Update();
/// \TODO : remove the following
- //if (verbose) reader->GetOutput()->PrintSelf(std::cout, vtkIndent(2));
+ if (verbose) {
+ std::cout << "reader->GetOutput() :" << std::endl;
+ reader->GetOutput()->PrintSelf(std::cout, vtkIndent(2));
+ }
ImageDataVector->push_back(reader->GetOutput() );
-
+
+ std::vector<vtkImageData*>::iterator it;
+ if (verbose)
+ for(it=ImageDataVector->begin(); it!=ImageDataVector->end(); ++it) {
+ std::cout << "-in vtkGdcm4DSplitter--------------------------" << std::endl;
+ (*it)->PrintSelf(std::cout, vtkIndent(2));
+ }
std::cout << std::endl;
}
return true;
}
+
+ void vtkGdcm4DSplitter::reorgXCoherentFileSetmap(GDCM_NAME_SPACE::XCoherentFileSetmap &xcm)
+ {
+ ELEM e;
+ std::vector<ELEM> vectElem;
+/*
+ typedef struct
+ {
+ std::string strIPP;
+ double dist;
+ GDCM_NAME_SPACE::File *file;
+ } ELEM;
+*/
+
+ bool Debug=true;
+
+ for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
+ i != xcm.end();
+ ++i)
+ {
+ if (verbose)
+ std::cout << "--- xCoherentName = [" << (*i).first << "]" << std::endl;
+
+ e.strIPP = (*i).first;
+ e.file = *(((*i).second)->begin()); // all the gdcm::File of a given xcm item *have* the same IPP; first one is enough
+ e.dist=0.0;
+ vectElem.push_back(e);
+ }
+ sortVectElem(&vectElem);
+
+ // now, create the final std::map !
+ // final_xcm<to_str(e.dist , xcm[e.strIPP]>
+ // xcm = final_xcm;
+ // check what we need to free !
+
+ int dist;
+ char c_dist[100];
+ std::string str_dist;
+ int lgr=vectElem.size();
+ GDCM_NAME_SPACE::XCoherentFileSetmap final_xcm;
+ for (int i2=0; i2<lgr; i2++)
+ {
+ dist = (vectElem[i2].dist*1000);
+ sprintf(c_dist,"%010d",dist);
+ str_dist = c_dist;
+/*
+ std::cout << "dist " << vectElem[i2].dist
+ << " str_dist " << str_dist
+ << " IPP " << vectElem[i2].strIPP
+ << std::endl;
+
+*/
+ final_xcm[str_dist] = xcm[vectElem[i2].strIPP];
+ }
+
+ /// \TODO : check what needs to be cleared // JPR
+
+ xcm = final_xcm;
+
+ }
+
+
+bool vtkGdcm4DSplitter::sortVectElem(std::vector<ELEM> *fileList)
+{
+//based on Jolinda Smith's algorithm
+
+//Tags always use the same coordinate system, where "x" is left
+//to right, "y" is posterior to anterior, and "z" is foot to head (RAH).
+
+ //iop is calculated based on the file file
+ float cosines[6];
+ double normal[3];
+ double ipp[3];
+ double dist;
+ double min = 0, max = 0;
+ bool first = true;
+
+ double ZSpacing; // useless here! // JPR
+ bool DirectOrder = true; // remove it!
+
+ ZSpacing = -1.0; // will be updated if process doesn't fail
+
+ //std::multimap<double,File *> distmultimap; // JPR
+ std::multimap<double,ELEM> distmultimap; // JPR
+
+ // Use a multimap to sort the distances from 0,0,0
+ //for ( FileList::const_iterator // JPR
+ for ( std::vector<ELEM>::iterator // JPR
+ it = fileList->begin();
+ it != fileList->end(); ++it )
+ {
+ //gdcmDebugMacro("deal with " << (*it)->file->GetFileName() );
+ if ( first )
+ {
+ (*it).file->GetImageOrientationPatient( cosines );
+
+ // The "Image Orientation Patient" tag gives the direction cosines
+ // for the rows and columns for the three axes defined above.
+ // Typical axial slices will have a value 1/0/0/0/1/0:
+ // rows increase from left to right,
+ // columns increase from posterior to anterior. This is your everyday
+ // "looking up from the bottom of the head with the eyeballs up" image.
+
+ // The "Image Position Patient" tag gives the coordinates of the first
+ // voxel in the image in the "RAH" coordinate system, relative to some
+ // origin.
+
+ // First, calculate the slice normal from IOP :
+
+ // You only have to do this once for all slices in the volume. Next,
+ // for each slice, calculate the distance along the slice normal
+ // using the IPP ("Image Position Patient") tag.
+ // ("dist" is initialized to zero before reading the first slice) :
+
+ normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
+ normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
+ normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
+
+ // For each slice (here : the first), calculate the distance along
+ // the slice normal using the IPP tag
+
+ ipp[0] = (*it).file->GetXOrigin();
+ ipp[1] = (*it).file->GetYOrigin();
+ ipp[2] = (*it).file->GetZOrigin();
+
+ dist = 0;
+ for ( int i = 0; i < 3; ++i )
+ {
+ dist += normal[i]*ipp[i];
+ }
+
+ //gdcmDebugMacro("dist : " << dist);
+ distmultimap.insert(std::pair<const double,ELEM>(dist, *it));
+
+ max = min = dist;
+ first = false;
+ }
+ else
+ {
+ // Next, for each slice, calculate the distance along the slice normal
+ // using the IPP tag
+ ipp[0] = (*it).file->GetXOrigin();
+ ipp[1] = (*it).file->GetYOrigin();
+ ipp[2] = (*it).file->GetZOrigin();
+
+ dist = 0;
+ for ( int i = 0; i < 3; ++i )
+ {
+ dist += normal[i]*ipp[i];
+ }
+
+ (*it).dist = dist; // JPR
+
+ distmultimap.insert(std::pair<const double,ELEM>(dist, *it));
+ //gdcmDebugMacro("dist : " << dist);
+ min = (min < dist) ? min : dist;
+ max = (max > dist) ? max : dist;
+ }
+ }
+
+ // gdcmDebugMacro("After parsing vector, nb of elements : " << fileList->size() );
+
+/*Useless here. // JPR
+
+ // Find out if min/max are coherent
+ if ( min == max )
+ {
+ gdcmWarningMacro("Looks like all images have the exact same image position. "
+ << "No PositionPatientOrdering sort performed. "
+ << "No 'ZSpacing' calculated! ");
+ return false;
+ }
+*/
+
+/* Useless here, 'split' already done. // JPR
+
+ // Check to see if image shares a common position
+ bool ok = true;
+ for (std::multimap<double, File *>::iterator it2 = distmultimap.begin();
+ it2 != distmultimap.end();
+ ++it2)
+ {
+
+ gdcmDebugMacro("Check if image shares a common position : " << ((*it2).second).file->GetFileName() );
+
+ if (distmultimap.count((*it2).first) != 1)
+ {
+ gdcmWarningMacro("File: ["
+ << ((*it2).second->GetFileName())
+ << "] : more than ONE file at distance: '"
+ << (*it2).first
+ << " (position is not unique!) "
+ << "No PositionPatientOrdering sort performed. "
+ << "No 'ZSpacing' calculated! ");
+
+ ok = false;
+ }
+ }
+ if (!ok)
+ {
+ if (! DropDuplicatePositions)
+ return false;
+ }
+
+*/
+
+// Now, we can calculate Z Spacing as the difference
+// between the "dist" values for the first two slices.
+
+// The following (un)-commented out code is let here
+// to be re-used by whomsoever is interested...
+
+ std::multimap<double, ELEM>::iterator it5 = distmultimap.begin();
+ double d1 = (*it5).first;
+ it5++;
+ double d2 = (*it5).first;
+ ZSpacing = d1-d2;
+ if (ZSpacing < 0.0)
+ ZSpacing = - ZSpacing;
+
+ fileList->clear(); // doesn't delete list elements, only nodes
+
+// Acording to user requierement, we sort direct order or reverse order.
+ if (DirectOrder)
+ {
+ for (std::multimap<double, ELEM>::iterator it3 = distmultimap.begin();
+ it3 != distmultimap.end();
+ ++it3)
+ {
+ fileList->push_back( (*it3).second );
+
+/* useless here! // JPR
+
+ if (DropDuplicatePositions)
+ {
+ // ImagePositionPatientOrdering wrong duplicates are found ???
+ // --> fixed. See comment
+
+ it3 = distmultimap.upper_bound((*it3).first); // skip all duplicates
+ // the upper_bound function increments the iterator to the next non-duplicate entry
+ // The for loop iteration also increments the iterator, which causes the code to skip every other image
+ // --> decrement the iterator after the upper_bound function call
+ it3--;
+ if (it3 == distmultimap.end() ) // if last image, stop iterate
+ break;
+ }
+*/
+ }
+ }
+ else // user asked for reverse order
+ {
+ std::multimap<double, ELEM>::const_iterator it4;
+ it4 = distmultimap.end();
+ do
+ {
+ it4--;
+ fileList->push_back( (*it4).second );
+
+/* useless here // JPR
+
+ if (DropDuplicatePositions) // skip all duplicates
+ {
+ // lower_bound finds the next element that is
+ // less than or *equal to* the current value!
+ //it4 = distmultimap.lower_bound((*it4).first);
+
+ // David Feng's fix
+ std::multimap<double, ELEM>::const_iterator itPrev = it4;
+ while (itPrev->first == it4->first)
+ --itPrev;
+ it4 = itPrev;
+
+ if (it4 == distmultimap.begin() ) // if first image, stop iterate
+ break;
+ }
+*/
+ } while (it4 != distmultimap.begin() );
+ }
+
+ distmultimap.clear();
+
+ return true;
+
+}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff