mitk::CylindricToCartesianFilter::~CylindricToCartesianFilter()
{
if(rt_pic!=NULL) mitkIpPicFree(rt_pic);
if(phit_pic!=NULL) mitkIpPicFree(phit_pic);
if(fr_pic!=NULL) mitkIpPicFree(fr_pic);
if(fphi_pic!=NULL) mitkIpPicFree(fphi_pic);
if(coneCutOff_pic!=NULL) mitkIpPicFree(coneCutOff_pic);
if(zt != NULL) free(zt);
if(fz != NULL) free (fz);
}
/**
3.1 Create a skeletonization of the segmentation and try to find a nice cut
3.1.1 Call a ipSegmentation algorithm to create a nice cut
3.1.2 Set the result of this algorithm as the feedback contour
*/
bool mitk::RegionGrowingTool::OnMousePressedInside( StateMachineAction*, InteractionEvent* interactionEvent, mitkIpPicDescriptor* workingPicSlice, int initialWorkingOffset)
{
if ( SegTool2D::CanHandleEvent(interactionEvent) < 1.0 )
return false;
mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
//const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent()); // checked in OnMousePressed
// 3.1.1. Create a skeletonization of the segmentation and try to find a nice cut
// apply the skeletonization-and-cut algorithm
// generate contour to remove
// set m_ReferenceSlice = NULL so nothing will happen during mouse move
// remember to fill the contour with 0 in mouserelease
mitkIpPicDescriptor* segmentationHistory = ipMITKSegmentationCreateGrowerHistory( workingPicSlice, m_LastWorkingSeed, NULL ); // free again
if (segmentationHistory)
{
tCutResult cutContour = ipMITKSegmentationGetCutPoints( workingPicSlice, segmentationHistory, initialWorkingOffset ); // tCutResult is a ipSegmentation type
mitkIpPicFree( segmentationHistory );
if (cutContour.cutIt)
{
int timestep = positionEvent->GetSender()->GetTimeStep();
// 3.1.2 copy point from float* to mitk::Contour
ContourModel::Pointer contourInImageIndexCoordinates = ContourModel::New();
contourInImageIndexCoordinates->Expand(timestep + 1);
contourInImageIndexCoordinates->SetClosed(true, timestep);
Point3D newPoint;
for (int index = 0; index < cutContour.deleteSize; ++index)
{
newPoint[0] = cutContour.deleteCurve[ 2 * index + 0 ] - 0.5;//correction is needed because the output of the algorithm is center based
newPoint[1] = cutContour.deleteCurve[ 2 * index + 1 ] - 0.5;//and we want our contour displayed corner based.
newPoint[2] = 0.0;
contourInImageIndexCoordinates->AddVertex( newPoint, timestep );
}
free(cutContour.traceline);
free(cutContour.deleteCurve); // perhaps visualize this for fun?
free(cutContour.onGradient);
ContourModel::Pointer contourInWorldCoordinates = FeedbackContourTool::BackProjectContourFrom2DSlice( m_WorkingSlice->GetGeometry(), contourInImageIndexCoordinates, true ); // true: sub 0.5 for ipSegmentation correction
FeedbackContourTool::SetFeedbackContour( *contourInWorldCoordinates );
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
m_FillFeedbackContour = true;
}
else
{
m_FillFeedbackContour = false;
}
}
else
{
m_FillFeedbackContour = false;
}
m_ReferenceSlice = NULL;
return true;
}
void mitk::PicFileReader::ConvertHandedness(mitkIpPicDescriptor* pic)
{
//left to right handed conversion
if(pic->dim>=3)
{
mitkIpPicDescriptor* slice=mitkIpPicCopyHeader(pic, NULL);
slice->dim=2;
size_t size=_mitkIpPicSize(slice);
slice->data=malloc(size);
size_t v, volumes = (pic->dim>3? pic->n[3] : 1);
size_t volume_size = size*pic->n[2];
for(v=0; v<volumes; ++v)
{
unsigned char *p_first=(unsigned char *)pic->data;
unsigned char *p_last=(unsigned char *)pic->data;
p_first+=v*volume_size;
p_last+=size*(pic->n[2]-1)+v*volume_size;
size_t i, smid=pic->n[2]/2;
for(i=0; i<smid;++i,p_last-=size, p_first+=size)
{
memcpy(slice->data, p_last, size);
memcpy(p_last, p_first, size);
memcpy(p_first, slice->data, size);
}
}
mitkIpPicFree(slice);
}
}
void mitk::PicFileReader::FillImage(Image::Pointer output)
{
mitkIpPicDescriptor *outputPic = mitkIpPicNew();
outputPic = CastToIpPicDescriptor(output, nullptr, outputPic);
mitkIpPicDescriptor *pic = mitkIpPicGet(const_cast<char *>(this->GetLocalFileName().c_str()), outputPic);
// comes upside-down (in MITK coordinates) from PIC file
ConvertHandedness(pic);
mitkIpPicTSV_t *tsv;
if ((tsv = mitkIpPicQueryTag(pic, "SOURCE HEADER")) != NULL)
{
if (tsv->n[0] > 1e+06)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag(pic, "SOURCE HEADER");
mitkIpPicFreeTag(tsvSH);
}
}
if ((tsv = mitkIpPicQueryTag(pic, "ICON80x80")) != NULL)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag(pic, "ICON80x80");
mitkIpPicFreeTag(tsvSH);
}
if ((tsv = mitkIpPicQueryTag(pic, "VELOCITY")) != NULL)
{
mitkIpPicDescriptor *header = mitkIpPicCopyHeader(pic, NULL);
header->data = tsv->value;
ConvertHandedness(header);
output->SetChannel(header->data, 1);
header->data = NULL;
mitkIpPicFree(header);
mitkIpPicDelTag(pic, "VELOCITY");
}
// Copy the memory to avoid mismatches of malloc() and delete[].
// mitkIpPicGet will always allocate a new memory block with malloc(),
// but MITK Images delete the data via delete[].
output->SetImportChannel(pic->data, 0, Image::CopyMemory);
pic->data = nullptr;
mitkIpPicFree(pic);
}
mitk::ImageDataItem::~ImageDataItem()
{
if(m_VtkImageData!=NULL)
m_VtkImageData->Delete();
if(m_PicDescriptor!=NULL)
{
m_PicDescriptor->data=NULL;
mitkIpPicFree(m_PicDescriptor);
}
if(m_Parent.IsNull())
{
if(m_ManageMemory)
delete [] m_Data;
}
}
mitkIpFloat8_t mitkIpFuncVarR ( mitkIpPicDescriptor *pic_old,
mitkIpUInt4_t *begin,
mitkIpUInt4_t *length )
{
mitkIpFloat8_t var; /* variance */
mitkIpPicDescriptor *pic_help;
pic_help = mitkIpFuncWindow ( pic_old, begin, length );
var = mitkIpFuncVar ( pic_help );
mitkIpPicFree ( pic_help );
return ( var );
}
mitkIpPicDescriptor *
MITKipPicGet( char *infile_name, mitkIpPicDescriptor *pic )
{
if(pic != NULL)
{
mitkIpPicDescriptor * tmpPic;
size_t sizePic, sizeTmpPic;
tmpPic = mitkIpPicGet(infile_name, NULL);
sizePic = _mitkIpPicSize(pic);
sizeTmpPic = _mitkIpPicSize(tmpPic);
if(sizePic != sizeTmpPic)
{
fprintf( stderr, "Critical: MITKipPicGet was given a pic with wrong size\n" );
return tmpPic;
}
memcpy(pic->data, tmpPic->data, sizePic);
pic->info->tags_head = tmpPic->info->tags_head;
tmpPic->info->tags_head = NULL;
mitkIpPicFree(tmpPic);
return pic;
}
else
return mitkIpPicGet(infile_name, pic);
}
mitk::Image::Pointer mitk::PicFileReader::CreateImage()
{
Image::Pointer output = Image::New();
std::string fileName = this->GetLocalFileName();
mitkIpPicDescriptor *header = mitkIpPicGetHeader(const_cast<char *>(fileName.c_str()), NULL);
if (!header)
{
mitkThrow() << "File could not be read.";
}
header = mitkIpPicGetTags(const_cast<char *>(fileName.c_str()), header);
int channels = 1;
mitkIpPicTSV_t *tsv;
if ((tsv = mitkIpPicQueryTag(header, "SOURCE HEADER")) != NULL)
{
if (tsv->n[0] > 1e+06)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag(header, "SOURCE HEADER");
mitkIpPicFreeTag(tsvSH);
}
}
if ((tsv = mitkIpPicQueryTag(header, "ICON80x80")) != NULL)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag(header, "ICON80x80");
mitkIpPicFreeTag(tsvSH);
}
if ((tsv = mitkIpPicQueryTag(header, "VELOCITY")) != NULL)
{
++channels;
mitkIpPicDelTag(header, "VELOCITY");
}
if (header == NULL || header->bpe == 0)
{
mitkThrow() << " Could not read file " << fileName;
}
// if pic image only 2D, the n[2] value is not initialized
unsigned int slices = 1;
if (header->dim == 2)
{
header->n[2] = slices;
}
// First initialize the geometry of the output image by the pic-header
SlicedGeometry3D::Pointer slicedGeometry = mitk::SlicedGeometry3D::New();
PicHelper::InitializeEvenlySpaced(header, header->n[2], slicedGeometry);
// if pic image only 3D, the n[3] value is not initialized
unsigned int timesteps = 1;
if (header->dim > 3)
{
timesteps = header->n[3];
}
slicedGeometry->ImageGeometryOn();
ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
timeGeometry->Initialize(slicedGeometry, timesteps);
// Cast the pic descriptor to ImageDescriptor and initialize the output
output->Initialize(CastToImageDescriptor(header));
output->SetTimeGeometry(timeGeometry);
mitkIpPicFree(header);
return output;
}
main( int argc, char *argv[] )
{
XtAppContext app_context;
Widget toplevel, bb, pic, annotation;
/*Widget button;*/
toplevel = XtVaAppInitialize( &app_context,
"Test",
NULL, 0,
&argc, argv,
fallback_resources,
NULL );
XtAddEventHandler( toplevel,
(EventMask)0,
True,_XEditResCheckMessages,
NULL );
n = 0;
XtSetArg( args[n], XmNheight, 400 ); n++;
XtSetArg( args[n], XmNwidth, 400 ); n++;
XtSetValues( toplevel, args, n );
bb = XmCreateDrawingArea( toplevel, "bb", args, n );
XtManageChild( bb );
n = 0;
XtSetArg( args[n], XmNx, 200 ); n++;
XtSetArg( args[n], XmNy, 100 ); n++;
annotation = XtCreateManagedWidget( "annotation",
xipAnnotationWidgetClass,
bb,
args, n );
XtAddCallback( annotation, XipNactivateCallback, activate, NULL );
n = 0;
XtSetArg( args[n], XmNx, 0 ); n++;
XtSetArg( args[n], XmNy, 0 ); n++;
XtSetArg( args[n], XipNquantisation, True ); n++;
XtSetArg( args[n], XipNpic, mitkIpPicGet( "../b.pic", NULL ) ); n++;
pic = XtCreateManagedWidget( "pic",
xipPicWidgetClass,
bb,
args, n );
/**************/
XtRealizeWidget( toplevel );
/**************/
{
mitkIpPicDescriptor *pic;
_mitkIpPicTagsElement_t *head;
mitkIpPicTSV_t *tsv;
pic = mitkIpPicGetTags( "../b.pic",
NULL );
tsv = mitkIpPicQueryTag( pic, "ANNOTATION" );
if( tsv != NULL )
{
head = tsv->value;
tsv = _mitkIpPicFindTag( head, "TEXT" )->tsv;
text = malloc( strlen(tsv->value) );
strcpy( text, tsv->value );
printf( "%s\n", text );
tsv = _mitkIpPicFindTag( head, "POSITION" )->tsv;
x = ((mitkIpUInt4_t *)(tsv->value))[0];
y = ((mitkIpUInt4_t *)(tsv->value))[1];
printf( "%i %i\n", x, y );
}
mitkIpPicFree( pic );
}
/**************/
XtVaSetValues( annotation,
XmNx, x,
XmNy, y,
NULL );
/**************/
XtAppMainLoop(app_context);
}
bool mitk::CorrectorAlgorithm::modifySegment( int lineStart, int lineEnd, ipMITKSegmentationTYPE state, mitkIpPicDescriptor *pic, int* _ofsArray )
{
// offsets for pixels right, top, left, bottom
int nbDelta4[4];
nbDelta4[0]=1; nbDelta4[1]=pic->n[0]; nbDelta4[1]*=-1; // necessary because of unsigned declaration of pic->n
nbDelta4[2]=-1; nbDelta4[3]=pic->n[0];
// offsets for pixels right, top-right, top, top-left left, bottom-left, bottom, bottom-right
int nbDelta8[8];
nbDelta8[0] = 1; nbDelta8[1] = nbDelta4[1]+1; nbDelta8[2] = nbDelta4[1]; nbDelta8[3] = nbDelta4[1]-1;
nbDelta8[4] = -1; nbDelta8[5] = nbDelta4[3]-1; nbDelta8[6] = nbDelta4[3]; nbDelta8[7] = nbDelta4[3]+1;
ipMITKSegmentationTYPE* picdata = static_cast<ipMITKSegmentationTYPE*>(pic->data);
ipMITKSegmentationTYPE saveStart = *(picdata + _ofsArray[lineStart]);
ipMITKSegmentationTYPE saveEnd = *(picdata + _ofsArray[lineEnd]);
ipMITKSegmentationTYPE newState = ((!state)&1) + 2; // probably equal to: ipMITKSegmentationTYPE newState = 3 - state;
// make two copies of pic:
mitkIpPicDescriptor *seg1 = mitkIpPicClone( pic );
mitkIpPicDescriptor *seg2 = mitkIpPicClone( pic );
int i;
// mark line in original
for (i=lineStart; i<=lineEnd; i++) {
*(picdata + _ofsArray[i]) = 3;
}
// mark the first side in copy 1:
bool firstPix = true;
bool modified;
int line = pic->n[0]; // #pixels in line
int maxOfs = (int)(line * pic->n[1]); // #pixels in slice
for (i=lineStart+1; i<lineEnd; i++) {
do {
modified = false;
for (int nb=0; nb<8; nb++) {
int nbOfs = _ofsArray[i] + nbDelta8[nb];
if ( nbOfs < 0 // above first line
|| nbOfs >= maxOfs // below last line
) continue;
ipMITKSegmentationTYPE nbVal = *(picdata + nbOfs);
ipMITKSegmentationTYPE destVal = *(((ipMITKSegmentationTYPE*)seg1->data) + nbOfs);
if (nbVal!=3 && destVal!=newState) { // get only neigbhours that are not part of the line itself
if (firstPix) {
*(((ipMITKSegmentationTYPE*)seg1->data) + nbOfs) = newState; // this one is used to mark the side!
firstPix = false;
modified = true;
}
else {
int tnb = 0;
while ( tnb < 4
&& ((nbOfs + nbDelta4[tnb]) >= 0) && ((nbOfs + nbDelta4[tnb]) < maxOfs)
&& *(((ipMITKSegmentationTYPE*)seg1->data) + nbOfs + nbDelta4[tnb]) != newState
)
tnb++;
if (tnb < 4 && ((nbOfs + nbDelta4[tnb]) >= 0) && ((nbOfs + nbDelta4[tnb]) < maxOfs) ) {
*(((ipMITKSegmentationTYPE*)seg1->data) + nbOfs) = newState; // we've got a buddy close
modified = true;
}
}
}
}
} while (modified);
}
// mark the other side in copy 2:
for (i=lineStart+1; i<lineEnd; i++) {
for (int nb=0; nb<4; nb++) {
int nbOfs = _ofsArray[i] + nbDelta4[nb];
if ( nbOfs < 0 // above first line
|| nbOfs >= maxOfs // below last line
) continue;
ipMITKSegmentationTYPE lineVal = *(picdata + nbOfs);
ipMITKSegmentationTYPE side1Val = *(((ipMITKSegmentationTYPE*)seg1->data) + nbOfs);
if (lineVal != 3 && side1Val != newState) {
*(((ipMITKSegmentationTYPE*)seg2->data) + nbOfs) = newState;
}
}
}
// take care of line ends for multiple segments:
*(((ipMITKSegmentationTYPE*)seg1->data) + _ofsArray[lineStart]) = newState;
*(((ipMITKSegmentationTYPE*)seg1->data) + _ofsArray[lineEnd]) = newState;
*(((ipMITKSegmentationTYPE*)seg2->data) + _ofsArray[lineStart]) = newState;
*(((ipMITKSegmentationTYPE*)seg2->data) + _ofsArray[lineEnd]) = newState;
// replace regions:
newState = (!state)&1;
int sizeRegion1 = 0, sizeRegion2 = 0;
for (i=lineStart+1; i<lineEnd; i++) {
if (*(((ipMITKSegmentationTYPE*)seg1->data) + _ofsArray[i]) != newState) {
sizeRegion1 += ipMITKSegmentationReplaceRegion4N( seg1, _ofsArray[i], newState );
}
if (*(((ipMITKSegmentationTYPE*)seg2->data) + _ofsArray[i]) != newState) {
sizeRegion2 += ipMITKSegmentationReplaceRegion4N( seg2, _ofsArray[i], newState );
}
}
// combine image:
//printf( "Size Region1 = %8i Size Region2 = %8i\n", sizeRegion1, sizeRegion2 );
int sizeDif;
ipMITKSegmentationTYPE *current, *segSrc;
if (sizeRegion1 < sizeRegion2) {
segSrc = (ipMITKSegmentationTYPE*)seg1->data;
sizeDif = sizeRegion2 - sizeRegion1;
}
else {
segSrc = (ipMITKSegmentationTYPE*)seg2->data;
sizeDif = sizeRegion1 - sizeRegion2;
}
modified = false;
if (sizeDif > 2*(lineEnd-lineStart)) {
// decision is safe enough:
ipMITKSegmentationTYPE *end = picdata + (pic->n[0]*pic->n[1]);
for (current = picdata; current<end; current++) {
if (*segSrc == newState) *current = newState;
segSrc++;
}
modified = true;
}
// restore line:
for (int i=lineStart+1; i<lineEnd; i++) {
*(picdata + _ofsArray[i]) = state;
}
// restore end points:
*(picdata + _ofsArray[lineStart]) = saveStart;
*(picdata + _ofsArray[lineEnd]) = saveEnd;
mitkIpPicFree( seg1 );
mitkIpPicFree( seg2 );
return modified;
}
void ipMITKSegmentationFree (mitkIpPicDescriptor* segmentation)
{
if (!segmentation) return;
mitkIpPicFree (segmentation);
}
mitkIpPicDescriptor *mitkIpFuncScale ( mitkIpPicDescriptor *pic_old,
mitkIpFloat8_t sc_fact[_mitkIpPicNDIM],
mitkIpFuncFlagI_t sc_kind )
{
mitkIpUInt4_t i; /* loop index */
mitkIpPicDescriptor *pic_new; /* pointer to scaled image */
char is_color=0;
/* check whether data are correct */
if(pic_old->bpe==24)
{
pic_old->bpe=8;
is_color=1;
}
if ( _mitkIpFuncError ( pic_old ) != mitkIpFuncOK ) return ( mitkIpFuncERROR );
if(is_color)
pic_old->bpe=24;
/* allocate pic_new */
pic_new = mitkIpPicCopyHeader ( pic_old, NULL );
if ( pic_new == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncPICNEW_ERROR );
return ( mitkIpFuncERROR );
}
/* copy scaling information to header of pic_new */
pic_new->dim = pic_old->dim;
for ( i = 0; i < pic_old->dim; i++ )
pic_new->n[i] =
( sc_fact[i] == 0 ) ?
pic_old->n[i] :
( mitkIpUInt4_t ) ( sc_fact[i] * pic_old->n[i] );
/* call scaling routines */
if ( sc_kind == mitkIpFuncScaleNN )
pic_new = _mitkIpFuncScNN ( pic_old, pic_new );
else if ( sc_kind == mitkIpFuncScaleBl ) {
pic_new = _mitkIpFuncScBL ( pic_old, pic_new );
/*printf("using NN due to error in _mitkIpFuncScaleBL ... ");
pic_new = _mitkIpFuncScNN ( pic_old, pic_new );*/
}
else
{
mitkIpPicFree ( pic_new );
_mitkIpFuncSetErrno ( mitkIpFuncFLAG_ERROR );
return ( mitkIpFuncERROR );
}
/* Copy Tags */
mitkIpFuncCopyTags(pic_new, pic_old);
return( pic_new );
}
mitkIpPicDescriptor *mitkIpFuncSqrt ( mitkIpPicDescriptor *pic_1,
mitkIpFuncFlagI_t keep,
mitkIpPicDescriptor *pic_return )
{
mitkIpPicDescriptor *pic_new; /* pointer to new image */
mitkIpUInt4_t i; /* loop index */
mitkIpFloat8_t min1, max1; /* extreme greyvalues of 1. image */
/* check image data */
if ( _mitkIpFuncError ( pic_1 ) != mitkIpFuncOK ) return ( mitkIpFuncERROR );
/* calculate max. and min. greyvalues of both images */
if ( mitkIpFuncExtr ( pic_1, &min1, &max1 ) != mitkIpFuncOK ) return ( mitkIpFuncERROR );
/* calculate max. and min. possible greyvalues for data type of images*/
/* find out data type of new iamge */
if ( keep == mitkIpFuncKeep )
{
pic_new = _mitkIpFuncMalloc ( pic_1, pic_return, mitkIpOVERWRITE );
if ( pic_new == NULL ) return ( mitkIpFuncERROR );
}
else if ( keep == mitkIpFuncNoKeep )
{
pic_new = mitkIpPicNew ();
pic_new->dim = pic_1->dim;
pic_new->bpe = 64;
pic_new->type = mitkIpPicFloat;
for ( i = 0; i < pic_new->dim; i++ )
pic_new->n[i] = pic_1->n[i];
}
else
{
_mitkIpFuncSetErrno ( mitkIpFuncFLAG_ERROR );
return ( mitkIpFuncERROR );
}
if ( pic_new == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncPICNEW_ERROR );
return ( mitkIpFuncERROR );
}
if ( keep == mitkIpFuncNoKeep )
pic_new->data = malloc ( _mitkIpPicSize ( pic_new ) );
if ( pic_new->data == NULL )
{
mitkIpPicFree ( pic_new );
_mitkIpFuncSetErrno ( mitkIpFuncMALLOC_ERROR );
return ( mitkIpFuncERROR );
}
/* macro to invert the picture (for all data types) */
mitkIpPicFORALL_1 ( SQRT1, pic_1, pic_new )
/* Copy Tags */
mitkIpFuncCopyTags(pic_new, pic_1);
return pic_new;
}
void mitk::PicFileReader::GenerateData()
{
Image::Pointer output = this->GetOutput();
// Check to see if we can read the file given the name or prefix
//
if ( m_FileName == "" && m_FilePrefix == "" )
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "One of FileName or FilePrefix must be non-empty");
}
if( m_FileName != "")
{
mitkIpPicDescriptor* outputPic = mitkIpPicNew();
outputPic = CastToIpPicDescriptor(output, outputPic);
mitkIpPicDescriptor* pic=MITKipPicGet(const_cast<char *>(m_FileName.c_str()),
outputPic);
// comes upside-down (in MITK coordinates) from PIC file
ConvertHandedness(pic);
mitkIpPicTSV_t *tsv;
if ( (tsv = mitkIpPicQueryTag( pic, "SOURCE HEADER" )) != NULL)
{
if(tsv->n[0]>1e+06)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag( pic, "SOURCE HEADER" );
mitkIpPicFreeTag(tsvSH);
}
}
if ( (tsv = mitkIpPicQueryTag( pic, "ICON80x80" )) != NULL)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag( pic, "ICON80x80" );
mitkIpPicFreeTag(tsvSH);
}
if ( (tsv = mitkIpPicQueryTag( pic, "VELOCITY" )) != NULL)
{
mitkIpPicDescriptor* header = mitkIpPicCopyHeader(pic, NULL);
header->data = tsv->value;
ConvertHandedness(header);
output->SetChannel(header->data, 1);
header->data = NULL;
mitkIpPicFree(header);
mitkIpPicDelTag( pic, "VELOCITY" );
}
//slice-wise reading
//currently much too slow.
//else
//{
// int sstart, smax;
// int tstart, tmax;
// sstart=output->GetRequestedRegion().GetIndex(2);
// smax=sstart+output->GetRequestedRegion().GetSize(2);
// tstart=output->GetRequestedRegion().GetIndex(3);
// tmax=tstart+output->GetRequestedRegion().GetSize(3);
// int s,t;
// for(s=sstart; s<smax; ++s)
// {
// for(t=tstart; t<tmax; ++t)
// {
// mitkIpPicDescriptor* pic=mitkIpPicGetSlice(const_cast<char *>(m_FileName.c_str()), NULL, t*smax+s+1);
// output->SetPicSlice(pic,s,t);
// }
// }
//}
}
else
{
int position;
mitkIpPicDescriptor* pic=NULL;
int zDim=(output->GetDimension()>2?output->GetDimensions()[2]:1);
printf("\n zdim is %u \n",zDim);
for (position = 0; position < zDim; ++position)
{
char fullName[1024];
sprintf(fullName, m_FilePattern.c_str(), m_FilePrefix.c_str(), m_StartFileIndex+position);
pic=MITKipPicGet(fullName, pic);
if(pic==NULL)
{
itkDebugMacro("Pic file '" << fullName << "' does not exist.");
}
/* FIXME else
if(output->SetPicSlice(pic, position)==false)
{
itkDebugMacro("Image '" << fullName << "' could not be added to Image.");
}*/
}
if(pic!=NULL)
mitkIpPicFree(pic);
}
}
mitkIpPicDescriptor *mitkIpFuncGausF ( mitkIpPicDescriptor *pic_old,
mitkIpUInt4_t len_mask,
mitkIpUInt4_t dim_mask,
mitkIpFuncFlagI_t border )
{
mitkIpPicDescriptor *pic_new; /* pointer to new image structure */
mitkIpPicDescriptor *pic_mask; /* pointer to mask */
mitkIpUInt4_t n[_mitkIpPicNDIM]; /* size of each dimension */
mitkIpUInt4_t ind[_mitkIpPicNDIM]; /* loop index vector */
mitkIpUInt4_t i, k; /* loop index */
mitkIpUInt4_t no_elem; /* number of mask elements */
mitkIpUInt4_t offset; /* offset of pixels */
mitkIpUInt4_t element; /* used to calculate mask elements */
mitkIpUInt4_t sum; /* sum of all mask elements */
mitkIpUInt4_t nn, nfac, kfac; /* used to calculate bin. coeff */
mitkIpUInt4_t *bin; /* binomial coeffizients */
/* check data */
if ( _mitkIpFuncError ( pic_old ) != mitkIpFuncOK ) return ( mitkIpFuncERROR );
if ( pic_old->dim < dim_mask || dim_mask < 1 )
{
_mitkIpFuncSetErrno ( mitkIpFuncDIMMASC_ERROR );
return ( mitkIpFuncERROR );
}
if ( len_mask % 2 != 1 )
{
_mitkIpFuncSetErrno ( mitkIpFuncDIM_ERROR );
return ( mitkIpFuncERROR );
}
/* calculate binomial coefficient */
bin = malloc ( len_mask * sizeof ( mitkIpUInt4_t ) );
if ( bin == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncMALLOC_ERROR );
return ( mitkIpFuncERROR );
}
nn = len_mask;
bin[0] = 1;
bin[nn-1] = 1;
nfac = 1;
kfac = 1;
for ( k = 1; k < nn-1; k++ )
{
kfac = k * kfac;
nfac = nfac * ( nn - k );
bin[k] = nfac / kfac;
}
/* initialize mask */
pic_mask = mitkIpPicNew();
if ( pic_mask == NULL )
{
free ( bin );
_mitkIpFuncSetErrno ( mitkIpFuncPICNEW_ERROR );
return ( mitkIpFuncERROR );
}
pic_mask->type = mitkIpPicFloat;
pic_mask->bpe = 64;
pic_mask->dim = dim_mask;
for ( i = 0; i < dim_mask; i++ ) pic_mask->n[i] = len_mask;
pic_mask->data = malloc ( _mitkIpPicSize ( pic_mask ) );
if ( pic_mask->data == NULL )
{
free ( bin );
mitkIpPicFree ( pic_mask );
_mitkIpFuncSetErrno ( mitkIpFuncPICNEW_ERROR );
return ( mitkIpFuncERROR );
}
/* initialize vectors */
for ( i = 0; i < pic_mask->dim; i++ )
n[i] = len_mask;
for ( i = pic_mask->dim; i < _mitkIpPicNDIM; i++ )
n[i] = 1;
/* calculate mask */
offset = 0;
sum = 0;
for ( ind[7] = 0; ind[7] < n[7]; ind[7]++ )
for ( ind[6] = 0; ind[6] < n[6]; ind[6]++ )
for ( ind[5] = 0; ind[5] < n[5]; ind[5]++ )
for ( ind[4] = 0; ind[4] < n[4]; ind[4]++ )
for ( ind[3] = 0; ind[3] < n[3]; ind[3]++ )
for ( ind[2] = 0; ind[2] < n[2]; ind[2]++ )
for ( ind[1] = 0; ind[1] < n[1]; ind[1]++ )
for ( ind[0] = 0; ind[0] < n[0]; ind[0]++ )
{
element = 1;
for ( i = 0; i < pic_mask->dim; i++ )
element = element * bin[ind[i]];
(( mitkIpFloat8_t * )pic_mask->data)[offset] =
( mitkIpFloat8_t ) element;
sum = sum + element;
offset++;
}
no_elem = _mitkIpPicElements ( pic_mask );
for ( i = 0; i < no_elem; i++ )
(( mitkIpFloat8_t * ) pic_mask->data ) [i] =
(( mitkIpFloat8_t * ) pic_mask->data ) [i] / ( mitkIpFloat8_t ) sum;
/* convolve image with Gausian mask */
pic_new = mitkIpFuncConv ( pic_old, pic_mask, border );
mitkIpPicFree ( pic_mask );
free ( bin );
/* Copy Tags */
mitkIpFuncCopyTags(pic_new, pic_old);
return ( pic_new );
}
void mitkIpPicPutSlice( const char *outfile_name, mitkIpPicDescriptor *pic, mitkIpUInt4_t slice )
{
mitkIpPicDescriptor *pic_in;
FILE *outfile;
size_t ignored;
pic_in = mitkIpPicGetHeader( outfile_name,
NULL );
if( pic_in == NULL )
{
if( slice == 1 )
{
mitkIpBool_t compression;
pic->n[pic->dim] = 1;
pic->dim += 1;
compression = mitkIpPicSetWriteCompression( mitkIpFalse );
mitkIpPicPut( outfile_name, pic );
mitkIpPicSetWriteCompression( compression );
pic->dim -= 1;
pic->n[pic->dim] = 0;
return;
}
else
return;
}
pic_in = mitkIpPicGetTags( outfile_name,
pic_in );
outfile = fopen( outfile_name, "r+b" );
if( outfile == NULL )
{
/*ipPrintErr( "mitkIpPicPut: sorry, error opening outfile\n" );*/
/*return();*/
}
if( pic->dim != pic_in->dim - 1 )
{
fclose( outfile );
return;
}
else if( pic->n[0] != pic_in->n[0] )
{
fclose( outfile );
return;
}
else if( pic->n[1] != pic_in->n[1] )
{
fclose( outfile );
return;
}
if( slice > pic_in->n[pic_in->dim-1] )
pic_in->n[pic_in->dim-1] += 1;
/* write outfile */
/*fseek( outfile, 0, SEEK_SET );*/
rewind( outfile );
ignored = fwrite( mitkIpPicVERSION, 1, sizeof(mitkIpPicTag_t), outfile );
fseek( outfile, sizeof(mitkIpUInt4_t), SEEK_CUR ); /* skip tags_len */
ignored = mitkIpFWriteLE( &(pic_in->type), sizeof(mitkIpUInt4_t), 1, outfile );
ignored = mitkIpFWriteLE( &(pic_in->bpe), sizeof(mitkIpUInt4_t), 1, outfile );
ignored = mitkIpFWriteLE( &(pic_in->dim), sizeof(mitkIpUInt4_t), 1, outfile );
ignored = mitkIpFWriteLE( pic_in->n, sizeof(mitkIpUInt4_t), pic_in->dim, outfile );
fseek( outfile, pic_in->info->pixel_start_in_file + _mitkIpPicSize(pic) * (slice - 1), SEEK_SET );
ignored = mitkIpFWriteLE( pic->data, pic->bpe / 8, _mitkIpPicElements(pic), outfile );
/*fseek( outfile, 0, SEEK_END );*/
fclose( outfile );
mitkIpPicFree(pic_in);
/*return();*/
}
mitkIpPicDescriptor*
ipMITKSegmentationCreateGrowerHistory( mitkIpPicDescriptor *seg, int startOfs, mitkIpPicDescriptor *histBuffer )
{
std::queue<int> ofsQueue;
if (!seg) return 0;
if (!histBuffer) {
histBuffer = mitkIpPicCopyHeader( seg, histBuffer );
histBuffer->type = mitkIpPicUInt;
histBuffer->bpe = 16;
mitkIpUInt4_t size = _mitkIpPicSize( histBuffer );
histBuffer->data = malloc( size );
memset( histBuffer->data, 0, size ); // clear buffer
}
else {
// check if dimension of histBuffer is valid, if not: change it!
if (histBuffer->n[0] != seg->n[0] || histBuffer->n[1] != seg->n[1]) {
histBuffer->n[0] = seg->n[0];
histBuffer->n[1] = seg->n[1];
mitkIpUInt4_t size = _mitkIpPicSize( histBuffer );
histBuffer->data = realloc( histBuffer->data, size );
if (histBuffer->data == 0) return 0;
memset( histBuffer->data, 0, size ); // clear buffer
}
}
// create a clear buffer to check wether a point has already been visited
// (seg cannot be modifier and histBuffer can contain any value)
mitkIpPicDescriptor *flagBuffer = mitkIpPicCopyHeader( seg, 0 );
mitkIpUInt4_t size = _mitkIpPicSize( flagBuffer );
flagBuffer->data = malloc( size );
memset( flagBuffer->data, 0, size );
*((mitkIpUInt1_t*)flagBuffer->data+startOfs) = 1; // flag pixel as visited
int line = seg->n[0];
int maxOfs = (int)(line * seg->n[1]);
int testOfs;
mitkIpUInt1_t segVal, flagVal;
int iteration = 0;
int currentWave = 1;
int nextWave = 0;
ofsQueue.push( startOfs );
while (!ofsQueue.empty()) {
int nextOfs = ofsQueue.front();
ofsQueue.pop();
currentWave--;
*((mitkIpUInt2_t*)histBuffer->data+nextOfs) = (mitkIpUInt2_t)(iteration+1); // seed point should get history = 1
// check right:
testOfs = nextOfs+1;
if (testOfs%line!=0) {
segVal = *((mitkIpUInt1_t*)seg->data+testOfs);
flagVal = *((mitkIpUInt1_t*)flagBuffer->data+testOfs);
if ( segVal != 0 && flagVal == 0) {
ofsQueue.push( testOfs );
*((mitkIpUInt1_t*)flagBuffer->data+testOfs) = 1; // flag pixel as visited
nextWave++;
}
}
// check top:
testOfs = nextOfs-line;
if (testOfs > 0) {
segVal = *((mitkIpUInt1_t*)seg->data+testOfs);
flagVal = *((mitkIpUInt1_t*)flagBuffer->data+testOfs);
if ( segVal != 0 && flagVal == 0) {
ofsQueue.push( testOfs );
*((mitkIpUInt1_t*)flagBuffer->data+testOfs) = 1; // flag pixel as visited
nextWave++;
}
}
// check left:
testOfs = nextOfs-1;
if (nextOfs%line!=0) {
segVal = *((mitkIpUInt1_t*)seg->data+testOfs);
flagVal = *((mitkIpUInt1_t*)flagBuffer->data+testOfs);
if ( segVal != 0 && flagVal == 0) {
ofsQueue.push( testOfs );
*((mitkIpUInt1_t*)flagBuffer->data+testOfs) = 1; // flag pixel as visited
nextWave++;
}
}
// check bottom:
testOfs = nextOfs+line;
if (testOfs < maxOfs) {
segVal = *((mitkIpUInt1_t*)seg->data+testOfs);
flagVal = *((mitkIpUInt1_t*)flagBuffer->data+testOfs);
if ( segVal != 0 && flagVal == 0) {
ofsQueue.push( testOfs );
*((mitkIpUInt1_t*)flagBuffer->data+testOfs) = 1; // flag pixel as visited
nextWave++;
}
}
// check for number of iterations:
if (currentWave == 0) {
currentWave = nextWave;
nextWave = 0;
iteration++;
}
}
mitkIpPicFree( flagBuffer );
return histBuffer;
}
int mitkImageTest(int argc, char* argv[])
{
MITK_TEST_BEGIN(mitkImageTest);
//Create Image out of nowhere
mitk::Image::Pointer imgMem;
mitk::PixelType pt(typeid(int));
unsigned int dim[]={100,100,20};
std::cout << "Testing creation of Image: ";
imgMem=mitk::Image::New();
if(imgMem.IsNull())
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing Initialize(const mitk::PixelType& type, unsigned int dimension, unsigned int *dimensions): ";
imgMem->Initialize(mitk::PixelType(typeid(int)), 3, dim);
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing IsInitialized(): ";
if(imgMem->IsInitialized()==false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing GetData(): ";
int *p = (int*)imgMem->GetData();
if(p==NULL)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Filling image: ";
unsigned int i;
unsigned int size = dim[0]*dim[1]*dim[2];
for(i=0; i<size; ++i, ++p)
*p= (signed int)i;
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Getting it again and compare with filled values: ";
int *p2 = (int*)imgMem->GetData();
if(p2==NULL)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
for(i=0; i<size; ++i, ++p2)
{
if(*p2!= (signed int)i )
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing IsInitialized(): ";
if(imgMem->IsInitialized()==false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing GetSliceData() and compare with filled values: ";
p2 = (int*)imgMem->GetSliceData(dim[2]/2)->GetData();
unsigned int xy_size = dim[0]*dim[1];
unsigned int start_mid_slice = (dim[2]/2)*xy_size;
for(i=0; i<xy_size; ++i, ++p2)
{
if(*p2!=(signed int)(i+start_mid_slice))
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
}
std::cout<<"[PASSED]"<<std::endl;
//----
mitkIpPicDescriptor *pic_slice=mitkIpPicClone(imgMem->GetSliceData(dim[2]/2)->GetPicDescriptor());
imgMem=mitk::Image::New();
std::cout << "Testing reinitializing via Initialize(const mitk::PixelType& type, unsigned int dimension, unsigned int *dimensions): ";
imgMem->Initialize(mitk::PixelType(typeid(int)), 3, dim);
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing slice-wise filling via SetPicSlice(): ";
for(i=0;i<dim[2];++i)
{
imgMem->SetPicSlice(pic_slice, i, 0, 0);
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Getting it again and compare with filled values: ";
p2 = (int*)imgMem->GetData();
if(p2==NULL)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
for(i=0; i<size; ++i, ++p2)
{
if(*p2!= (signed int)((i%xy_size)+start_mid_slice))
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing IsInitialized(): ";
if(imgMem->IsInitialized()==false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Setting a copy of the volume once again: ";
imgMem->SetPicVolume(mitkIpPicClone(imgMem->GetVolumeData(0)->GetPicDescriptor()),0);
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Set a slice with different content via SetPicSlice(): ";
memset(pic_slice->data,0,xy_size*sizeof(int));
imgMem->SetPicSlice(pic_slice, 1);
std::cout << "Getting the volume again and compare the check the changed slice: ";
p2 = (int*)imgMem->GetData();
if(p2==NULL)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
p2+=xy_size;
for(i=0; i<xy_size; ++i, ++p2)
{
if(*p2!=0)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Setting volume again: ";
imgMem->SetVolume(imgMem->GetData());
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Set a slice with different content via SetSlice(): ";
memset(pic_slice->data,0,xy_size*sizeof(int));
imgMem->SetSlice(pic_slice->data, 0);
std::cout << "Getting the volume again and compare the check the changed slice: ";
p2 = (int*)imgMem->GetData();
if(p2==NULL)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
for(i=0; i<xy_size; ++i, ++p2)
{
if(*p2!=0)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
}
std::cout<<"[PASSED]"<<std::endl;
//std::cout << "Testing SetVolume(): ";
//imgMem->SetVolume(data);
//std::cout<<"[PASSED]"<<std::endl;
mitkIpPicFree(pic_slice);
//-----------------
// geometry information for image
mitk::Point3D origin;
mitk::Vector3D right, bottom;
mitk::Vector3D spacing;
mitk::FillVector3D(origin, 17.0, 19.92, 7.83);
mitk::FillVector3D(right, 1.0, 2.0, 3.0);
mitk::FillVector3D(bottom, 0.0, -3.0, 2.0);
mitk::FillVector3D(spacing, 0.78, 0.91, 2.23);
std::cout << "Testing InitializeStandardPlane(rightVector, downVector, spacing): " << std::flush;
mitk::PlaneGeometry::Pointer planegeometry = mitk::PlaneGeometry::New();
planegeometry->InitializeStandardPlane(100, 100, right, bottom, &spacing);
planegeometry->SetOrigin(origin);
std::cout << "done" << std::endl;
std::cout << "Testing Initialize(const mitk::PixelType& type, const mitk::Geometry3D& geometry, unsigned int slices) with PlaneGeometry and GetData(): ";
imgMem->Initialize(mitk::PixelType(typeid(int)), *planegeometry);
p = (int*)imgMem->GetData();
if(p==NULL)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing Initialize(const mitk::PixelType& type, int sDim, const mitk::PlaneGeometry& geometry) and GetData(): ";
imgMem->Initialize(mitk::PixelType(typeid(int)), 40, *planegeometry);
p = (int*)imgMem->GetData();
if(p==NULL)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
//-----------------
// testing origin information and methods
std::cout << "Testing correctness of origin via GetGeometry()->GetOrigin(): ";
if( mitk::Equal(imgMem->GetGeometry()->GetOrigin(), origin) == false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing correctness of origin via GetTimeSlicedGeometry()->GetOrigin(): ";
if( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetOrigin(), origin) == false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
mitk::FillVector3D(origin, 37.0, 17.92, 27.83);
std::cout << "Setting origin via SetOrigin(origin): ";
imgMem->SetOrigin(origin);
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing correctness of changed origin via GetGeometry()->GetOrigin(): ";
if( mitk::Equal(imgMem->GetGeometry()->GetOrigin(), origin) == false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing correctness of changed origin via GetTimeSlicedGeometry()->GetOrigin(): ";
if( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetOrigin(), origin) == false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing correctness of changed origin via GetSlicedGeometry()->GetGeometry2D(0)->GetOrigin(): ";
if( mitk::Equal(imgMem->GetSlicedGeometry()->GetGeometry2D(0)->GetOrigin(), origin) == false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
//-----------------
// testing spacing information and methods
std::cout << "Testing correctness of spacing via GetGeometry()->GetSpacing(): ";
if( mitk::Equal(imgMem->GetGeometry()->GetSpacing(), spacing) == false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing correctness of spacing via GetTimeSlicedGeometry()->GetSpacing(): ";
if( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetSpacing(), spacing) == false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
mitk::FillVector3D(spacing, 7.0, 0.92, 1.83);
std::cout << "Setting spacing via SetSpacing(spacing): ";
imgMem->SetSpacing(spacing);
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing correctness of changed spacing via GetGeometry()->GetSpacing(): ";
if( mitk::Equal(imgMem->GetGeometry()->GetSpacing(), spacing) == false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing correctness of changed spacing via GetTimeSlicedGeometry()->GetSpacing(): ";
if( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetSpacing(), spacing) == false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing correctness of changed spacing via GetSlicedGeometry()->GetGeometry2D(0)->GetSpacing(): ";
if( mitk::Equal(imgMem->GetSlicedGeometry()->GetGeometry2D(0)->GetSpacing(), spacing) == false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
//-----------------
MITK_TEST_OUTPUT(<< "Testing SetImportChannel");
mitk::Image::Pointer vecImg = mitk::Image::New();
vecImg->Initialize(*imgMem->GetPixelType().GetTypeId(), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/ );
vecImg->SetImportChannel(imgMem->GetData(), 0, mitk::Image::CopyMemory );
vecImg->SetImportChannel(imgMem->GetData(), 1, mitk::Image::CopyMemory );
std::cout<<"[PASSED]"<<std::endl;
MITK_TEST_OUTPUT(<< " Testing whether IsValidSlice returns valid after SetImportChannel");
MITK_TEST_CONDITION_REQUIRED( vecImg->IsValidSlice(0,0,1) , "");
MITK_TEST_OUTPUT(<< " Testing whether CopyMemory worked");
MITK_TEST_CONDITION_REQUIRED(imgMem->GetData() != vecImg->GetData(), "");
MITK_TEST_OUTPUT(<< " Testing destruction after SetImportChannel");
vecImg = NULL;
std::cout<<"[PASSED]"<<std::endl;
//-----------------
MITK_TEST_OUTPUT(<< "Testing initialization via vtkImageData");
MITK_TEST_OUTPUT(<< " Setting up vtkImageData");
vtkImageData* vtkimage = vtkImageData::New();
vtkimage->Initialize();
vtkimage->SetDimensions( 2, 3, 4);
double vtkorigin[] = {-350,-358.203, -1363.5};
vtkimage->SetOrigin(vtkorigin);
mitk::Point3D vtkoriginAsMitkPoint;
mitk::vtk2itk(vtkorigin, vtkoriginAsMitkPoint);
double vtkspacing[] = {1.367, 1.367, 2};
vtkimage->SetSpacing(vtkspacing);
vtkimage->SetScalarType( VTK_SHORT );
vtkimage->AllocateScalars();
std::cout<<"[PASSED]"<<std::endl;
MITK_TEST_OUTPUT(<< " Testing mitk::Image::Initialize(vtkImageData*, ...)");
mitk::Image::Pointer mitkByVtkImage = mitk::Image::New();
mitkByVtkImage ->Initialize(vtkimage);
MITK_TEST_CONDITION_REQUIRED(mitkByVtkImage->IsInitialized(), "");
MITK_TEST_OUTPUT(<< " vtkimage->Delete");
vtkimage->Delete();
std::cout<<"[PASSED]"<<std::endl;
MITK_TEST_OUTPUT(<< " Testing whether spacing has been correctly initialized from vtkImageData");
mitk::Vector3D spacing2 = mitkByVtkImage->GetGeometry()->GetSpacing();
mitk::Vector3D vtkspacingAsMitkVector;
mitk::vtk2itk(vtkspacing, vtkspacingAsMitkVector);
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(spacing2,vtkspacingAsMitkVector), "");
MITK_TEST_OUTPUT(<< " Testing whether GetSlicedGeometry(0)->GetOrigin() has been correctly initialized from vtkImageData");
mitk::Point3D origin2 = mitkByVtkImage->GetSlicedGeometry(0)->GetOrigin();
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), "");
MITK_TEST_OUTPUT(<< " Testing whether GetGeometry()->GetOrigin() has been correctly initialized from vtkImageData");
origin2 = mitkByVtkImage->GetGeometry()->GetOrigin();
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), "");
MITK_TEST_OUTPUT(<< " Testing whether GetTimeSlicedGeometry()->GetOrigin() has been correctly initialized from vtkImageData");
origin2 = mitkByVtkImage->GetTimeSlicedGeometry()->GetOrigin();
MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), "");
// TODO test the following initializers on channel-incorporation
// void mitk::Image::Initialize(const mitk::PixelType& type, unsigned int dimension, unsigned int *dimensions, unsigned int channels)
// void mitk::Image::Initialize(const mitk::PixelType& type, int sDim, const mitk::Geometry2D& geometry2d, bool flipped, unsigned int channels, int tDim )
// void mitk::Image::Initialize(const mitk::Image* image)
// void mitk::Image::Initialize(const mitkIpPicDescriptor* pic, int channels, int tDim, int sDim)
//mitk::Image::Pointer vecImg = mitk::Image::New();
//vecImg->Initialize(PixelType(typeid(float), 6, itk::ImageIOBase::SYMMETRICSECONDRANKTENSOR), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/, false /*shiftBoundingBoxMinimumToZero*/ );
//vecImg->Initialize(PixelType(typeid(itk::Vector<float,6>)), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/, false /*shiftBoundingBoxMinimumToZero*/ );
// testing access by index coordinates and by world coordinates
mitk::DataNode::Pointer node;
mitk::DataNodeFactory::Pointer nodeReader = mitk::DataNodeFactory::New();
MITK_TEST_CONDITION_REQUIRED(argc == 2, "Check if test image is accessible!");
const std::string filename = std::string(argv[1]);
try
{
nodeReader->SetFileName(filename);
nodeReader->Update();
node = nodeReader->GetOutput();
}
catch(...) {
MITK_TEST_FAILED_MSG(<< "Could not read file for testing: " << filename);
return NULL;
}
mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
// test by index coordinates
mitk::Index3D index;
mitk::FillVector3D(index, 55, 39, 50);
MITK_TEST_OUTPUT(<< "Testing mitk::Image::GetPixelValueByIndex");
double val = image->GetPixelValueByIndex(index);
MITK_TEST_CONDITION_REQUIRED( mitk::Equal(val,112.22475433349609), "");
//test by world coordinates
MITK_TEST_OUTPUT(<< "Testing mitk::Image::GetPixelValueByWorldCoordinate");
mitk::Point3D point;
mitk::FillVector3D(point, -5.93752, 18.7199, 6.74218);
val = image->GetPixelValueByWorldCoordinate(point);
MITK_TEST_CONDITION_REQUIRED( mitk::Equal(val,94.456184387207031), "");
MITK_TEST_OUTPUT(<< "Convert to index and access value by mitk::Image::GetPixelValueByIndex again");
mitk::Index3D index2;
image->GetGeometry()->WorldToIndex(point, index2);
float val2 = image->GetPixelValueByIndex(index2);
MITK_TEST_CONDITION_REQUIRED( mitk::Equal(val2,94.456184387207031), "");
//access via itk
MITK_TEST_OUTPUT(<< "Test conversion to itk::Image");
typedef itk::Image<float,3> ItkFloatImage3D;
ItkFloatImage3D::Pointer itkimage;
mitk::CastToItkImage(image, itkimage);
std::cout<<"[PASSED]"<<std::endl;
MITK_TEST_OUTPUT(<< "Testing world->itk-physical->world consistency");
mitk::Point3D itkPhysicalPoint;
image->GetGeometry()->WorldToItkPhysicalPoint(point, itkPhysicalPoint);
mitk::Point3D backTransformedPoint;
image->GetGeometry()->ItkPhysicalPointToWorld(itkPhysicalPoint, backTransformedPoint);
MITK_TEST_CONDITION_REQUIRED( mitk::Equal(point,backTransformedPoint), "");
MITK_TEST_OUTPUT(<< "Compare value of pixel returned by mitk in comparison to itk");
itk::Index<3> idx;
itkimage->TransformPhysicalPointToIndex(itkPhysicalPoint, idx);
float valByItk = itkimage->GetPixel(idx);
MITK_TEST_CONDITION_REQUIRED( mitk::Equal(valByItk,94.456184387207031), "");
mitk::Image::Pointer cloneImage = image->Clone();
MITK_TEST_CONDITION_REQUIRED(cloneImage->GetDimension() == image->GetDimension(), "Clone (testing dimension)");
MITK_TEST_CONDITION_REQUIRED(cloneImage->GetPixelType() == image->GetPixelType(), "Clone (testing pixel type)");
for (unsigned int i = 0u; i < cloneImage->GetDimension(); ++i)
{
MITK_TEST_CONDITION_REQUIRED(cloneImage->GetDimension(i) == image->GetDimension(i), "Clone (testing dimension " << i << ")");
}
MITK_TEST_END();
return EXIT_SUCCESS;
}
void mitk::CylindricToCartesianFilter::GenerateData()
{
mitk::Image::ConstPointer input = this->GetInput();
mitk::Image::Pointer output = this->GetOutput();
mitk::ImageTimeSelector::Pointer timeSelector=mitk::ImageTimeSelector::New();
timeSelector->SetInput(input);
mitkIpPicDescriptor* pic_transformed=NULL;
pic_transformed = mitkIpPicNew();
pic_transformed->dim=3;
pic_transformed->bpe = output->GetPixelType().GetBpe();
//pic_transformed->type = output->GetPixelType().GetType();
pic_transformed->n[0] = output->GetDimension(0);
pic_transformed->n[1] = output->GetDimension(1);
pic_transformed->n[2] = output->GetDimension(2);
pic_transformed->data=malloc(_mitkIpPicSize(pic_transformed));
int nstart, nmax;
int tstart, tmax;
tstart=output->GetRequestedRegion().GetIndex(3);
nstart=output->GetRequestedRegion().GetIndex(4);
tmax=tstart+output->GetRequestedRegion().GetSize(3);
nmax=nstart+output->GetRequestedRegion().GetSize(4);
if(zt==NULL)
{
timeSelector->SetChannelNr(nstart);
timeSelector->SetTimeNr(tstart);
buildTransformShortCuts(input->GetDimension(0),input->GetDimension(1), input->GetDimension(2), output->GetDimension(0), rt_pic, phit_pic, fr_pic, fphi_pic, zt, fz);
// query the line limiting the sector
a=b=0;
mitk::FloatProperty::Pointer prop;
prop = dynamic_cast<mitk::FloatProperty*>(input->GetProperty("SECTOR LIMITING LINE SLOPE").GetPointer());
if (prop.IsNotNull() )
a = prop->GetValue();
prop = dynamic_cast<mitk::FloatProperty*>(input->GetProperty("SECTOR LIMITING LINE OFFSET").GetPointer());
if (prop.IsNotNull() )
b = prop->GetValue();
buildConeCutOffShortCut(input->GetDimension(0),input->GetDimension(1), rt_pic, fr_pic, a, b, coneCutOff_pic);
// mitkIpPicPut("C:\\temp\\rt_90.pic",rt_pic);
//mitkIpPicPut("C:\\temp\\coneCutOff.pic", coneCutOff_pic);
}
int n,t;
for(n=nstart;n<nmax;++n)//output->GetNumberOfChannels();++n)
{
timeSelector->SetChannelNr(n);
for(t=tstart;t<tmax;++t)
{
timeSelector->SetTimeNr(t);
timeSelector->Update();
// Cast to pic descriptor for the timeSelector image
mitkIpPicDescriptor* timeSelectorPic = mitkIpPicNew();
CastToIpPicDescriptor( timeSelector->GetOutput(), timeSelectorPic );
_mitkIpPicFreeTags(pic_transformed->info->tags_head);
pic_transformed->info->tags_head = _mitkIpPicCloneTags(timeSelectorPic->info->tags_head);
if(input->GetDimension(2)>1)
{
mitkIpPicTypeMultiplex9(_transform, timeSelectorPic , pic_transformed, m_OutsideValue, (float*)fr_pic->data, (float*)fphi_pic->data, fz, (short *)rt_pic->data, (unsigned int *)phit_pic->data, zt, coneCutOff_pic);
// mitkIpPicPut("1trf.pic",pic_transformed);
}
else
{
mitkIpPicDescriptor *doubleSlice = mitkIpPicCopyHeader( timeSelectorPic , NULL);
doubleSlice->dim=3;
doubleSlice->n[2]=2;
doubleSlice->data=malloc(_mitkIpPicSize(doubleSlice));
memcpy(doubleSlice->data, timeSelectorPic->data, _mitkIpPicSize(doubleSlice)/2);
mitkIpPicTypeMultiplex9(_transform, doubleSlice, pic_transformed, m_OutsideValue, (float*)fr_pic->data, (float*)fphi_pic->data, fz, (short *)rt_pic->data, (unsigned int *)phit_pic->data, zt, coneCutOff_pic);
mitkIpPicFree(doubleSlice);
}
output->SetVolume(pic_transformed->data, t, n);
}
}
//mitkIpPicPut("outzzzzzzzz.pic",pic_transformed);
mitkIpPicFree(pic_transformed);
m_TimeOfHeaderInitialization.Modified();
}
mitkIpPicDescriptor *mitkIpFuncSubC ( mitkIpPicDescriptor *pic_old,
mitkIpFloat8_t value,
mitkIpFuncFlagI_t keep,
mitkIpPicDescriptor *pic_return )
{
mitkIpPicDescriptor *pic_new; /* pointer to new image */
mitkIpFloat8_t max_gv; /* max. possible greyvalue */
mitkIpFloat8_t min_gv; /* min. possible greyvalue */
mitkIpFloat8_t min1, max1; /* extreme greyvalues of 1. image */
mitkIpFloat8_t smin, smax; /* product of extreme greyvalues */
/* check image data */
if ( _mitkIpFuncError ( pic_old ) != mitkIpFuncOK ) return ( mitkIpFuncERROR );
/* check value */
if ( value == 0. ) return ( pic_old );
/*
else if ( value == 0. )
{
_mitkIpFuncSetErrno ( mitkIpFuncDATA_ERROR );
return ( mitkIpFuncERROR );
}
*/
/* calculate max. and min. possible greyvalues for data type of images*/
if ( _mitkIpFuncExtT ( pic_old->type, pic_old->bpe, &min_gv, &max_gv ) != mitkIpFuncOK )
return ( mitkIpFuncERROR );
/* find out data type of new iamge */
if ( keep == mitkIpFuncKeep )
{
pic_new = _mitkIpFuncMalloc ( pic_old, pic_return, mitkIpOVERWRITE );
if ( pic_new == NULL ) return ( mitkIpFuncERROR );
}
else if ( keep == mitkIpFuncNoKeep )
{
/* calculate max. and min. greyvalues of both images */
if ( mitkIpFuncExtr ( pic_old, &min1, &max1 ) != mitkIpFuncOK ) return ( mitkIpFuncERROR );
smax = max1 - value;
smin = min1 - value;
/* change image type of images of type mitkIpPicInt */
if ( pic_old->type == mitkIpPicInt )
{
if ( smax < max_gv && smin > min_gv )
{
pic_new = mitkIpPicCopyHeader ( pic_old, NULL );
}
else
{
pic_new = mitkIpPicCopyHeader ( pic_old, NULL );
pic_new->type = mitkIpPicFloat;
pic_new->bpe = 64;
_mitkIpFuncExtT ( pic_new->type, pic_new->bpe, &min_gv, &max_gv );
}
}
/* change image type of images of type mitkIpPicUInt */
else if ( pic_old->type == mitkIpPicUInt )
{
if ( smax < max_gv && smin > min_gv )
{
pic_new = mitkIpPicCopyHeader ( pic_old, NULL );
}
else
{
pic_new = mitkIpPicCopyHeader ( pic_old, NULL );
pic_new->type = mitkIpPicInt;
pic_new->bpe = 16;
_mitkIpFuncExtT ( pic_new->type, pic_new->bpe, &min_gv, &max_gv );
if ( smax > max_gv || smin < min_gv )
{
pic_new->type = mitkIpPicFloat;
pic_new->bpe = 64;
_mitkIpFuncExtT ( pic_new->type, pic_new->bpe, &min_gv, &max_gv );
}
}
}
/* change image type of images of type mitkIpPicUInt */
else if ( pic_old->type == mitkIpPicFloat )
{
pic_new = mitkIpPicCopyHeader ( pic_old, NULL );
}
else
{
_mitkIpFuncSetErrno ( mitkIpFuncTYPE_ERROR );
return ( mitkIpFuncERROR );
}
}
else
{
_mitkIpFuncSetErrno ( mitkIpFuncFLAG_ERROR );
return ( mitkIpFuncERROR );
}
if ( pic_new == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncPICNEW_ERROR );
return ( mitkIpFuncERROR );
}
if ( keep == mitkIpFuncNoKeep )
pic_new->data = malloc ( _mitkIpPicSize ( pic_new ) );
if ( pic_new->data == NULL )
{
mitkIpPicFree ( pic_new );
_mitkIpFuncSetErrno ( mitkIpFuncMALLOC_ERROR );
return ( mitkIpFuncERROR );
}
/* macro to invert the picture (for all data types) */
if ( keep == mitkIpFuncNoKeep )
mitkIpPicFORALL_2 ( SUBC, pic_old, pic_new, value )
if ( keep == mitkIpFuncKeep )
mitkIpPicFORALL_2 ( SUBC3, pic_old, pic_new, value )
/* Copy Tags */
mitkIpFuncCopyTags(pic_new, pic_old);
return pic_new;
}
int mitkImageSliceSelectorTest(int argc, char* argv[])
{
int slice_nr = 1;
std::cout << "Loading file: ";
if(argc==0)
{
std::cout<<"no file specified [FAILED]"<<std::endl;
return EXIT_FAILURE;
}
mitk::Image::Pointer image = NULL;
mitk::DataNodeFactory::Pointer factory = mitk::DataNodeFactory::New();
try
{
std::cout<<argv[1]<<std::endl;
factory->SetFileName( argv[1] );
factory->Update();
if(factory->GetNumberOfOutputs()<1)
{
std::cout<<"file could not be loaded [FAILED]"<<std::endl;
return EXIT_FAILURE;
}
mitk::DataNode::Pointer node = factory->GetOutput( 0 );
image = dynamic_cast<mitk::Image*>(node->GetData());
if(image.IsNull())
{
std::cout<<"file not an image - test will not be applied [PASSED]"<<std::endl;
std::cout<<"[TEST DONE]"<<std::endl;
return EXIT_SUCCESS;
}
}
catch ( itk::ExceptionObject & ex )
{
std::cout << "Exception: " << ex << "[FAILED]" << std::endl;
return EXIT_FAILURE;
}
if(image->GetDimension(2)<2)
slice_nr = 0;
//Take a slice
mitk::ImageSliceSelector::Pointer slice = mitk::ImageSliceSelector::New();
slice->SetInput(image);
slice->SetSliceNr(slice_nr);
slice->Update();
std::cout << "Testing IsInitialized(): ";
if(slice->GetOutput()->IsInitialized()==false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing IsSliceSet(): ";
if(slice->GetOutput()->IsSliceSet(0)==false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
if(itksys::SystemTools::LowerCase(itksys::SystemTools::GetFilenameExtension(argv[1])).find(".pic")!=std::string::npos)
{
std::cout << "Testing whether the slice is identical with a slice loaded by mitkIpPicGetSlice:";
mitkIpPicDescriptor *picslice = mitkIpPicGetSlice(argv[1], NULL, (image->GetDimension(2)-1-slice_nr)+1);
int i, size = _mitkIpPicSize(picslice);
char * p1 = (char*)slice->GetPic()->data;
char * p2 = (char*)picslice->data;
//picslice->info->write_protect=mitkIpFalse;
//mitkIpPicPut("C:\\1aaaaIPPIC.pic", picslice);
//mitkIpPicPut("C:\\1aaaaSEL.pic", slice->GetPic());
for(i=0; i<size; ++i, ++p1, ++p2)
{
if((*p1) != (*p2))
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
}
std::cout<<"[PASSED]"<<std::endl;
mitkIpPicFree(picslice);
}
try
{
std::cout << "Testing another, smaller (!!) input with the same slice-selector(): ";
//Use CylindricToCartesianFilter
mitk::CylindricToCartesianFilter::Pointer cyl2cart = mitk::CylindricToCartesianFilter::New();
cyl2cart->SetInput(image);
//the output size of this filter is smaller than the of the input!!
cyl2cart->SetTargetXSize( 64 );
//Use the same slice-selector again, this time to take a slice of the filtered image
//which is smaller than the one of the old input!!
slice->SetInput(cyl2cart->GetOutput());
slice->SetSliceNr(1);
//The requested region is still the old one,
//therefore the following results in most ITK versions
//in an exception!
slice->Update();
//If no exception occured, check that the requested region is now
//the one of the smaller image
if(cyl2cart->GetOutput()->GetLargestPossibleRegion().GetSize()[0]!=64)
{
std::cout<<"Part 1 [FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"Part 1 (without exception) [PASSED] ";
//Check that the size of the output is now the one of the smaller image
if((cyl2cart->GetOutput()->GetDimensions()[0]!=64) || (cyl2cart->GetOutput()->GetDimensions()[1]!=64))
{
std::cout<<"Part 1b [FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"Part 1b [PASSED] ";
}
catch ( itk::ExceptionObject &err)
{
std::cout<<"Part 1(with expected exception) ... seems to be not ITK 2.0.0 [PASSED]"<<std::endl;
std::cout<<err<<std::endl;
//after such an exception, we need to call ResetPipeline.
slice->ResetPipeline();
}
try
{
slice->UpdateLargestPossibleRegion();
}
catch ( itk::ExceptionObject )
{
std::cout<<"Part 2 [FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"Part 2 [PASSED]"<<std::endl;
std::cout << "Testing IsInitialized(): ";
if(slice->GetOutput()->IsInitialized()==false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing IsSliceSet(): ";
if(slice->GetOutput()->IsSliceSet(0)==false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
if(image->GetDimension(3) > 1)
{
int time=image->GetDimension(3)-1;
std::cout << "Testing 3D+t: Setting time to " << time << ": ";
slice->SetTimeNr(time);
if(slice->GetTimeNr()!=time)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing 3D+t: Updating slice: ";
slice->Update();
if(slice->GetOutput()->IsInitialized()==false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing 3D+t: IsSliceSet(): ";
if(slice->GetOutput()->IsSliceSet(0)==false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
std::cout << "Testing 3D+t: First slice in reader available: ";
if(image->IsSliceSet(0, time)==false)
{
std::cout<<"[FAILED]"<<std::endl;
return EXIT_FAILURE;
}
std::cout<<"[PASSED]"<<std::endl;
}
std::cout<<"[TEST DONE]"<<std::endl;
return EXIT_SUCCESS;
}
void mitk::DopplerToStrainRateFilter::GenerateData()
{
mitk::Image::ConstPointer input = this->GetInput();
mitk::Image::Pointer output = this->GetOutput();
mitk::Point3iProperty::Pointer pointProp;
pointProp = dynamic_cast<mitk::Point3iProperty*>(input->GetProperty("ORIGIN").GetPointer());
if (pointProp.IsNotNull() )
{
m_Origin = pointProp->GetValue();
}
MITK_INFO << "compute Strain Rate Image .... " << std::endl
<< " origin[0]=" << m_Origin[0] << " origin[1]=" << m_Origin[1] << " origin[2]=" << m_Origin[2] << std::endl
<< " distance=" << m_Distance << std::endl
<< " NoStrainIntervall=" << m_NoStrainInterval << std::endl;
const Vector3D & spacing = input->GetSlicedGeometry()->GetSpacing();
// MITK_INFO << " in: xres=" << spacing[0] << " yres=" << spacing[1] << " zres=" << spacing[2] << std::endl;
mitk::ImageTimeSelector::Pointer timeSelector=mitk::ImageTimeSelector::New();
timeSelector->SetInput(input);
mitkIpPicDescriptor* picStrainRate;
picStrainRate = mitkIpPicNew();
picStrainRate->dim=3;
picStrainRate->bpe = output->GetPixelType().GetBpe();
//picStrainRate->type = output->GetPixelType().GetType();
picStrainRate->n[0] = output->GetDimension(0);
picStrainRate->n[1] = output->GetDimension(1);
picStrainRate->n[2] = output->GetDimension(2);
picStrainRate->data=malloc(_mitkIpPicSize(picStrainRate));
int xDim = picStrainRate->n[0];
int yDim = picStrainRate->n[1];
int zDim = picStrainRate->n[2];
long slice_size = xDim*yDim;
long vol_size = slice_size*zDim;
mitkIpPicDescriptor *picDoppler;
int x,y,z;//,time; // loop-counter
int strainRate; // the computed Strain Rate
int v1,v2; // velocity and Point p1 and p2
float alpha; // the beam-angle, angle betwen current point and beam-point
float dx=0, dy=0; // projection of this->distance to x- and y-axis
int x1; // a square, where the velocity v1 lies in
int y1; // the points are used for interpolation
int minStrainRate=128, maxStrainRate=128;
int n, nmax;
int t, tmax;
t = output->GetRequestedRegion().GetIndex(3);
n = output->GetRequestedRegion().GetIndex(4);
MITK_INFO << "t = " <<t << " n = " << n << std::endl;
tmax = t + output->GetRequestedRegion().GetSize(3);
nmax = n + output->GetRequestedRegion().GetSize(4);
MITK_INFO << "tmax = "<< tmax << " nmax = " << nmax << std::endl;
if (m_Distance<1) m_Distance=1;
for(;n<nmax;n++)//output->GetNumberOfChannels();++n)
{
timeSelector->SetChannelNr(n);
MITK_INFO << "computing chanel n = " << n << std::endl;
for(t=0;t<tmax;t++)
{
MITK_INFO << "computing time slot t = " << t << std::endl;
timeSelector->SetTimeNr(t);
timeSelector->Update();
// Cast to pic descriptor for the timeSelector image
mitkIpPicDescriptor* timeSelectorPic = mitkIpPicNew();
CastToIpPicDescriptor( timeSelector->GetOutput(), timeSelectorPic );
_mitkIpPicFreeTags(picStrainRate->info->tags_head);
picStrainRate->info->tags_head = _mitkIpPicCloneTags(timeSelectorPic->info->tags_head);
//#define WRITE_ANGLE_PIC
#ifdef WRITE_ANGLE_PIC
mitkIpPicDescriptor *anglePic;
mitkIpBool_t isAnglePicWritten = mitkIpFalse;
anglePic = mitkIpPicNew();
anglePic->type = mitkIpPicInt;
anglePic->bpe = 8;
anglePic->dim = 2;
anglePic->n[0] = xDim;
anglePic->n[1] = yDim;
anglePic->data = (mitkIpInt1_t *)calloc(xDim*yDim,sizeof(mitkIpInt1_t));
#endif
picDoppler = timeSelectorPic;
picDoppler = mitkIpFuncGausF( picDoppler, 5,2 , mitkIpFuncBorderOld ) ;
for (z=0 ; z<zDim ; z++) {
for (y=1; y<yDim; y++) {
if (y<m_Origin[1]) continue; // cannot compute StrainRate above Transducer-Position
for (x=0; x<xDim; x++) {
if ((m_Origin[0] - x)==0) { // winkelhalbierende
int yDistanceInUnits = (int)( m_Distance/spacing[1]);
int yTmp = ( (y-yDistanceInUnits)<0 ) ? 0 : (y-yDistanceInUnits);
v1 = ((mitkIpUInt1_t *)picDoppler->data)[z*slice_size + yTmp*xDim + x] ;
v2 = ((mitkIpUInt1_t *)picDoppler->data)[z*slice_size + y*xDim + x] ;
} else {
// compute angle to transducer position
// m_Origin is given in units, not in mm
alpha = atan( (float) (m_Origin[0] - x) / (float) (m_Origin[1] - y) );
// m_Distance is given in mm
dx = -sin(alpha) * m_Distance;
dy = -cos(alpha) * m_Distance;
// convert to units
dx = dx/spacing[0];
dy = dy/spacing[1];
//#define WEIGTHED
#ifdef WEIGTHED
weightX = dx - floor(dx);
weightY = dy - floor(dy);
dxFloor = (int) floor(dx);
dyFloor = (int) floor(dy);
x1 = x + dxFloor; // lower left
y1 = y + dyFloor;
x2 = x + (dxFloor+1); // lower right
y2 = y + dyFloor;
x3 = x + (dxFloor+1); // upper right
y3 = y + (dyFloor+1);
x4 = x + dxFloor; // upper left
y4 = y + (dyFloor+1);
vTmp1 = ((mitkIpUInt1_t *)picDoppler->data)[z*slice_size + y1*xDim + x1];
vTmp2 = ((mitkIpUInt1_t *)picDoppler->data)[z*slice_size + y2*xDim + x2];
vTmp3 = ((mitkIpUInt1_t *)picDoppler->data)[z*slice_size + y3*xDim + x3];
vTmp4 = ((mitkIpUInt1_t *)picDoppler->data)[z*slice_size + y4*xDim + x4];
v1 = (int) ((1-weightX)*(1-weightY)*vTmp1 + weightX*(1-weightY)*vTmp2 + weightX*weightY*vTmp3 + (1-weightX)*weightY*vTmp4);
v2 = ((mitkIpUInt1_t *)picDoppler->data)[z*slice_size + y*xDim + x] ;
#else
x1 = (int)(x + dx);
y1 = (int)(y + dy);
if (y1<0) y1=0;
#endif
v1 = ((mitkIpUInt1_t *)picDoppler->data)[z*slice_size + y1*xDim + x1];
v2 = ((mitkIpUInt1_t *)picDoppler->data)[z*slice_size + y*xDim + x] ;
}
if (v1==128) { // schaue in Gegenrichtung, falls keine SRI hier berechenbar
x1 = (int)(x - dx);
y1 = (int)(y - dy);
if (y1>yDim) y1=yDim;
//swap v1 and v2, otherwise StrainRate is calculate in false direction
v1 = v2;
v2 = ((mitkIpUInt1_t *)picDoppler->data)[z*slice_size + y1*xDim + x1];
}
if ( (v1==0 ) || (v2==0) || // wenn keine Geschwindigkeit vorhanden
// oder wenn nur ganz kleine Geschwindigkeit vorhanden
(v1>=(128-m_NoStrainInterval) && v1<=(128+m_NoStrainInterval)) ||
(v2>=(128-m_NoStrainInterval) && v2<=(128+m_NoStrainInterval))) {
strainRate = 128; // this means no deformation
// this is neccessay due to the Cyl2Cart filter
} else {
strainRate = (int)( (v1 - v2)/2 + 128 );
if (strainRate==128) strainRate=129;
}
if (strainRate < minStrainRate && strainRate > 0 )
minStrainRate = strainRate;
if (strainRate > maxStrainRate)
maxStrainRate = strainRate;
if (strainRate<0 ) {
//strainRate = -strainRate;
MITK_INFO << " error: neg. strainRate ... exit() " << std::endl
<< " x=" << x << " y=" << y << " z=" << z << std::endl
<< " v1=" << v1 << " v2=" << v2 << " dist=" << m_Distance << std::endl
<< " sr=" << strainRate << std::endl;
exit(0);
}
((mitkIpUInt1_t *)picStrainRate->data)[t*vol_size + z*slice_size + y*xDim + x]=strainRate;
// cout << "z: " << z << " y: " << y << " x: " << x << " strainrate: " << strainRate << endl;
#ifdef WRITE_ANGLE_PIC
// if (!isAnglePicWritten)
// ((mitkIpInt1_t *)anglePic->data)[y*xDim + x] = (int) ( (alpha/1.6)*128);
if (!isAnglePicWritten)
((mitkIpInt1_t *)anglePic->data)[y*xDim + x] = (int) ( dx);
#endif
} // x
} // y
//isAnglePicWritten = mitkIpTrue;
} // z
//isStrainComputed = mitkIpTrue;
std::string filenameD;
filenameD ="doppler.pic";
mitkIpPicPut(const_cast<char *>(filenameD.c_str()),picDoppler);
#define WRITE_STRAIN_PIC
#ifdef WRITE_STRAIN_PIC
char tmpfilename[100];
sprintf(tmpfilename,"strain%d.pic",t);;
mitkIpPicPut(tmpfilename,picStrainRate);
#endif
#ifdef WRITE_ANGLE_PIC
std::string filename2;
filename2="angle.pic";
mitkIpPicPut(const_cast<char *>(filename2.c_str()),anglePic);
#endif
((mitkIpUInt1_t *)picStrainRate->data)[0]=0;
((mitkIpUInt1_t *)picStrainRate->data)[1]=255;
output->SetVolume(picStrainRate->data, t, n);
}
}
mitkIpPicFree(picStrainRate);
#define WRITE_STRAIN_PIC
#ifdef WRITE_STRAIN_PIC
// Get the StrainRate ipPic descriptor
picStrainRate = mitkIpPicNew();
CastToIpPicDescriptor( output, picStrainRate );
std::string filename;
filename ="strain.pic";
mitkIpPicPut(const_cast<char *>(filename.c_str()),picStrainRate);
#endif
MITK_INFO << "Strain Rate Image computed.... " << std::endl
<< " minStrainRate: " << minStrainRate << std::endl
<< " maxStrainRate: " << maxStrainRate << std::endl;
}
void mitk::PicFileReader::GenerateOutputInformation()
{
Image::Pointer output = this->GetOutput();
if ((output->IsInitialized()) && (this->GetMTime() <= m_ReadHeaderTime.GetMTime()))
return;
itkDebugMacro(<<"Reading file for GenerateOutputInformation()" << m_FileName);
// Check to see if we can read the file given the name or prefix
//
if ( m_FileName == "" && m_FilePrefix == "" )
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "One of FileName or FilePrefix must be non-empty");
}
if( m_FileName != "")
{
mitkIpPicDescriptor* header=mitkIpPicGetHeader(const_cast<char *>(m_FileName.c_str()), NULL);
if ( !header )
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "File could not be read.");
}
header=MITKipPicGetTags(const_cast<char *>(m_FileName.c_str()), header);
int channels = 1;
mitkIpPicTSV_t *tsv;
if ( (tsv = mitkIpPicQueryTag( header, "SOURCE HEADER" )) != NULL)
{
if(tsv->n[0]>1e+06)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag( header, "SOURCE HEADER" );
mitkIpPicFreeTag(tsvSH);
}
}
if ( (tsv = mitkIpPicQueryTag( header, "ICON80x80" )) != NULL)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag( header, "ICON80x80" );
mitkIpPicFreeTag(tsvSH);
}
if ( (tsv = mitkIpPicQueryTag( header, "VELOCITY" )) != NULL)
{
++channels;
mitkIpPicDelTag( header, "VELOCITY" );
}
if( header == NULL || header->bpe == 0)
{
itk::ImageFileReaderException e(__FILE__, __LINE__);
itk::OStringStream msg;
msg << " Could not read file "
<< m_FileName.c_str();
e.SetDescription(msg.str().c_str());
throw e;
return;
}
// First initialize the geometry of the output image by the pic-header
SlicedGeometry3D::Pointer slicedGeometry = mitk::SlicedGeometry3D::New();
PicHelper::InitializeEvenlySpaced(header, header->n[2], slicedGeometry);
// if pic image only 3D, the n[3] value is not initialized
unsigned int timesteps = 1;
if( header->dim > 3 )
timesteps = header->n[3];
TimeSlicedGeometry::Pointer timeSliceGeometry = TimeSlicedGeometry::New();
timeSliceGeometry->InitializeEvenlyTimed(slicedGeometry, timesteps);
timeSliceGeometry->ImageGeometryOn();
// Cast the pic descriptor to ImageDescriptor and initialize the output
output->Initialize( CastToImageDescriptor(header));
output->SetGeometry( timeSliceGeometry );
mitkIpPicFree ( header );
}
else
{
int numberOfImages=0;
m_StartFileIndex=0;
mitkIpPicDescriptor* header=NULL;
char fullName[1024];
while(m_StartFileIndex<10)
{
sprintf(fullName, m_FilePattern.c_str(), m_FilePrefix.c_str(), m_StartFileIndex+numberOfImages);
FILE * f=fopen(fullName,"r");
if(f==NULL)
{
//already found an image?
if(numberOfImages>0)
break;
//no? let's increase start
++m_StartFileIndex;
}
else
{
fclose(f);
//only open the header of the first file found,
//@warning what to do when images do not have the same size??
if(header==NULL)
{
header=mitkIpPicGetHeader(fullName, NULL);
header=MITKipPicGetTags(fullName, header);
}
++numberOfImages;
}
}
printf("\n numberofimages %d\n",numberOfImages);
if(numberOfImages==0)
{
itk::ImageFileReaderException e(__FILE__, __LINE__);
itk::OStringStream msg;
msg << "no images found";
e.SetDescription(msg.str().c_str());
throw e;
return;
}
//@FIXME: was ist, wenn die Bilder nicht alle gleich gross sind?
if(numberOfImages>1)
{
printf("\n numberofimages %d > 1\n",numberOfImages);
header->dim=3;
header->n[2]=numberOfImages;
}
printf(" \ninitialisize output\n");
output->Initialize( CastToImageDescriptor(header) );
mitkIpPicFree ( header );
}
m_ReadHeaderTime.Modified();
}
mitkIpPicDescriptor *mitkIpFuncSubI ( mitkIpPicDescriptor *pic_1,
mitkIpPicDescriptor *pic_2,
mitkIpFuncFlagI_t keep,
mitkIpPicDescriptor *pic_return )
{
mitkIpPicDescriptor *pic_new; /* pointer to new image */
mitkIpUInt4_t i; /* loop index */
mitkIpFloat8_t max_gv; /* max. possible greyvalue */
mitkIpFloat8_t min_gv; /* min. possible greyvalue */
mitkIpFloat8_t min1, max1; /* extreme greyvalues of 1. image */
mitkIpFloat8_t min2, max2; /* extreme greyvalues of 2. image */
mitkIpFloat8_t smin, smax; /* product of extreme greyvalues */
/* ckeck whether data are correct */
if ( _mitkIpFuncError ( pic_1 ) != mitkIpFuncOK ) return ( mitkIpFuncERROR );
if ( _mitkIpFuncError ( pic_2 ) != mitkIpFuncOK ) return ( mitkIpFuncERROR );
/* check whether images have the same size */
if ( ( pic_1->type != pic_2->type ) || ( pic_1->bpe != pic_2->bpe ) )
{
_mitkIpFuncSetErrno ( mitkIpFuncUNFIT_ERROR );
return NULL;
}
if ( pic_1->dim == pic_2->dim )
for ( i = 0; i < _mitkIpPicNDIM; i++ )
{
if ( pic_1->n[i] != pic_2->n[i] )
{
_mitkIpFuncSetErrno ( mitkIpFuncUNFIT_ERROR );
return NULL;
}
}
else
{
_mitkIpFuncSetErrno ( mitkIpFuncUNFIT_ERROR );
return NULL;
}
/* calculate max. and min. possible greyvalues for data type of images*/
if ( _mitkIpFuncExtT ( pic_1->type, pic_1->bpe, &min_gv, &max_gv ) != mitkIpFuncOK )
return ( mitkIpFuncERROR );
/* find out data type of new iamge */
if ( keep == mitkIpFuncKeep )
{
pic_new = _mitkIpFuncMalloc ( pic_1, pic_return, mitkIpOVERWRITE );
if ( pic_new == NULL ) return ( mitkIpFuncERROR );
}
else if ( keep == mitkIpFuncNoKeep )
{
/* calculate max. and min. greyvalues of both images */
if ( mitkIpFuncExtr ( pic_1, &min1, &max1 ) != mitkIpFuncOK ) return ( mitkIpFuncERROR );
if ( mitkIpFuncExtr ( pic_2, &min2, &max2 ) != mitkIpFuncOK ) return ( mitkIpFuncERROR );
smax = max1 - max2;
smin = min1 - min2;
/* change image type of images of type mitkIpPicInt */
if ( pic_1->type == mitkIpPicInt )
{
if ( smax < max_gv && smin > min_gv )
{
pic_new = mitkIpPicCopyHeader ( pic_1, NULL );
}
else
{
pic_new = mitkIpPicCopyHeader ( pic_1, NULL );
pic_new->type = mitkIpPicFloat;
pic_new->bpe = 64;
_mitkIpFuncExtT ( pic_new->type, pic_new->bpe, &min_gv, &max_gv );
}
}
/* change image type of images of type mitkIpPicUInt */
else if ( pic_1->type == mitkIpPicUInt )
{
if ( smax < max_gv && smin > min_gv )
{
pic_new = mitkIpPicCopyHeader ( pic_1, NULL );
}
else
{
pic_new = mitkIpPicCopyHeader ( pic_1, NULL );
pic_new->type = mitkIpPicInt;
pic_new->bpe = 16;
_mitkIpFuncExtT ( pic_new->type, pic_new->bpe, &min_gv, &max_gv );
if ( smax > max_gv || smin < min_gv )
{
pic_new->type = mitkIpPicFloat;
pic_new->bpe = 64;
_mitkIpFuncExtT ( pic_new->type, pic_new->bpe, &min_gv, &max_gv );
}
}
}
/* change image type of images of type mitkIpPicUInt */
else if ( pic_1->type == mitkIpPicFloat )
{
pic_new = mitkIpPicCopyHeader ( pic_1, NULL );
}
else
{
_mitkIpFuncSetErrno ( mitkIpFuncTYPE_ERROR );
return ( mitkIpFuncERROR );
}
}
else
{
_mitkIpFuncSetErrno ( mitkIpFuncFLAG_ERROR );
return ( mitkIpFuncERROR );
}
if ( pic_new == NULL )
{
_mitkIpFuncSetErrno ( mitkIpFuncPICNEW_ERROR );
return ( mitkIpFuncERROR );
}
if ( keep == mitkIpFuncNoKeep )
pic_new->data = malloc ( _mitkIpPicSize ( pic_new ) );
if ( pic_new->data == NULL )
{
mitkIpPicFree ( pic_new );
_mitkIpFuncSetErrno ( mitkIpFuncMALLOC_ERROR );
return ( mitkIpFuncERROR );
}
/* macro to invert the picture (for all data types) */
if ( keep == mitkIpFuncNoKeep )
mitkIpPicFORALL_2 ( SUBI, pic_1, pic_2, pic_new )
else if ( keep == mitkIpFuncKeep )
mitkIpPicFORALL_2 ( SUBI3, pic_1, pic_2, pic_new )
/* Copy Tags */
mitkIpFuncCopyTags(pic_new, pic_1);
return pic_new;
}
