void
VolumeCollectionTester::Test ( Tcl_Interp* iInterp ) {
stringstream ssError;
try {
string fnMRI = "test_data/bertT1.mgz";
VolumeCollection* vol = new VolumeCollection();
vol->SetFileName( fnMRI );
MRI* mri = const_cast<MRI*>(vol->GetMRI());
Assert( (vol->GetTypeDescription() == "Volume"),
"GetTypeDescription didn't return Volume" );
DataManager dataMgr = DataManager::GetManager();
MRILoader mriLoader = dataMgr.GetMRILoader();
Assert( 1 == mriLoader.CountLoaded(),
"CountLoaded didn't return 1" );
Assert( 1 == mriLoader.CountReferences(mri),
"CountReferences didn't return 1" );
char* fnMRIC = strdup( fnMRI.c_str() );
MRI* mriComp = MRIread( fnMRIC );
Assert( (MRImatch( mriComp, mri )), "MRImatch failed for load" );
MRIfree( &mriComp );
// Save it in /tmp, load it, and match it again.
string fnSave( "/tmp/test.mgz" );
vol->Save( fnSave );
VolumeCollection* testVol = new VolumeCollection();
testVol->SetFileName( fnSave );
MRI* testMri = const_cast<MRI*>(testVol->GetMRI());
Assert( (MRImatch( testMri, mri )), "MRImatch failed for load after save");
// Make an ROI and make sure it's a volume ROI.
try {
int roiID = vol->NewROI();
ScubaROIVolume* roi =
dynamic_cast<ScubaROIVolume*>(&ScubaROI::FindByID( roiID ));
roi = NULL;
} catch (...) {
throw( runtime_error("typecast failed for NewROI") );
}
// Try our conversions.
Point3<float> world;
Point3<float> data;
Point3<int> index;
world.Set( -50, 0, -80 );
vol->RASToMRIIndex( world.xyz(), index.xyz() );
{
stringstream ssError;
ssError << "RASToMRIIndex failed. world "
<< world << " index " << index;
Assert( (index.x() == 178 && index.y() == 208 && index.z() == 128),
ssError.str() );
}
// Set a transform that scales the volume up by 2x in the world.
ScubaTransform dataTransform;
dataTransform.SetMainTransform( 2, 0, 0, 0,
0, 2, 0, 0,
0, 0, 2, 0,
0, 0, 0, 1 );
vol->SetDataToWorldTransform( dataTransform.GetID() );
world.Set( -50, 0, -80 );
vol->RASToDataRAS( world.xyz(), data.xyz() );
{
stringstream ssError;
ssError << "RASToDataRAS failed. world "
<< world << " data " << data;
Assert( ((FEQUAL(data.x(),-25)) &&
(FEQUAL(data.y(),0)) &&
(FEQUAL(data.z(),-40))),
ssError.str() );
}
vol->RASToMRIIndex( world.xyz(), index.xyz() );
if ( index.x() != 153 || index.y() != 168 || index.z() != 128 ) {
cerr << "RASToMRIIndex with data transform failed. world "
<< world << " index " << index << endl;
throw( runtime_error( "failed" ) );
}
world.Set( -50, 0, -80 );
VolumeLocation loc( vol->MakeVolumeLocationFromRAS( world.xyz() ) );
if ( !vol->IsInBounds( loc ) ) {
stringstream ssError;
ssError << "IsInBounds failed. world " << world;
throw( runtime_error( ssError.str() ) );
}
world.Set( -1000, 0, 0 );
VolumeLocation loc2( vol->MakeVolumeLocationFromRAS( world.xyz() ) );
if ( vol->IsInBounds( loc2 ) ) {
stringstream ssError;
ssError << "IsInBounds failed. world " << world;
throw( runtime_error( ssError.str() ) );
}
dataTransform.SetMainTransform( 2, 0, 0, 0,
0, 2, 0, 0,
0, 0, 2, 0,
0, 0, 0, 1 );
vol->SetDataToWorldTransform( dataTransform.GetID() );
world.Set( 0, -1000, -254 );
VolumeLocation loc3( vol->MakeVolumeLocationFromRAS( world.xyz() ) );
if ( vol->IsInBounds( loc3 ) ) {
stringstream ssError;
vol->RASToMRIIndex( world.xyz(), index.xyz() );
ssError << "IsRASInMRIBounds failed. world " << world
<< " index " << index;
throw( runtime_error( ssError.str() ) );
}
{
// Create a new one from template.
VolumeCollection* vol2 = new VolumeCollection();
vol2->MakeUsingTemplate( vol->GetID(), -1 );
Assert( (vol->mVoxelSize[0] == vol2->mVoxelSize[0] &&
vol->mVoxelSize[1] == vol2->mVoxelSize[1] &&
vol->mVoxelSize[2] == vol2->mVoxelSize[2]),
"NewUsingTemplate failed, vol2 didn't match vol's voxelsize" );
Assert( (vol->GetDataType() == vol2->GetDataType()),
"NewUsingTemplate(-1) failed, vol2 didn't match vol's data type" );
delete vol2;
}
{
VolumeCollection* vol2 = new VolumeCollection();
vol2->MakeUsingTemplate( vol->GetID(), MRI_FLOAT );
Assert( (vol->mVoxelSize[0] == vol2->mVoxelSize[0] &&
vol->mVoxelSize[1] == vol2->mVoxelSize[1] &&
vol->mVoxelSize[2] == vol2->mVoxelSize[2]),
"NewUsingTemplate failed, vol2 didn't match vol's voxelsize" );
Assert( (MRI_FLOAT == vol2->GetDataType()),
"NewUsingTemplate(float) failed, vol2 wasn't a float" );
int idx[3] = { 0, 0, 0 };
VolumeLocation loc( vol2->MakeVolumeLocationFromIndex( idx ) );
vol2->SetMRIValue( loc, 0.6789 );
float value = vol2->GetMRINearestValue(loc);
stringstream ssError;
ssError << "NewUsingTemplate(float) failed value comparison, "
<< "was expecting 0.6789 but got " << value;
Assert( (fabs(0.6789 - value) < 0.00001), ssError.str() );
delete vol2;
}
{
VolumeCollection* vol2 = NULL;
try {
vol2 = new VolumeCollection();
vol2->MakeUsingTemplate( vol->GetID(), 10000 );
throw runtime_error( "MakeUsingTemplate(10000) didn't throw an error");
}
catch(...) {}
delete vol2;
}
dataTransform.SetMainTransform( 1, 0, 0, 0,
0, 1, 0, 0,
0, 0, 1, 0,
0, 0, 0, 1 );
vol->SetDataToWorldTransform( dataTransform.GetID() );
// FindRASPointsInSquare
{
Point3<float> sqRAS[4], cRAS;
sqRAS[0].Set( 0, -3, 71 );
sqRAS[1].Set( 0, 1, 71 );
sqRAS[2].Set( 0, 1, 67 );
sqRAS[3].Set( 0, -3, 67 );
cRAS.Set( 0, -1, 69 );
list<Point3<float> > points;
vol->FindRASPointsInSquare( cRAS.xyz(),
sqRAS[0].xyz(), sqRAS[1].xyz(),
sqRAS[2].xyz(), sqRAS[3].xyz(),
0, points );
list<Point3<float> >::iterator tPoint;
for ( tPoint = points.begin(); tPoint != points.end(); ++tPoint ) {
Point3<float> pRAS = *tPoint;
stringstream ssMsg;
ssMsg << "Failed: " << pRAS << " outside of square";
Assert( ( pRAS[0] == 0 &&
(pRAS[1] >= -3 && pRAS[1] <= 1) &&
(pRAS[2] >= 67 && pRAS[2] <= 71) ),
ssMsg.str() );
}
}
// VoxelIntersectsSegment
{
Point3<int> idx;
Point3<float> segIdxA, segIdxB;
Point3<float> intIdx;
idx.Set( 5, 5, 5 );
float aSegments[6][3] = { {3, 5.5, 5.5}, {6, 5.5, 5.5},
{5.5, 3, 5.5}, {5.5, 6, 5.5},
{5.5, 5.5, 3}, {5.5, 5.5, 6} };
for ( int nSegment = 0; nSegment < 6; nSegment += 2 ) {
segIdxA.Set( aSegments[nSegment] );
segIdxB.Set( aSegments[nSegment+1] );
VectorOps::IntersectionResult rInt =
vol->VoxelIntersectsSegment( idx, segIdxA, segIdxB, intIdx );
if ( VectorOps::intersect != rInt ) {
cerr << "Failed VoxelIntersectsSegment test: idx " << idx
<< ", seg " << segIdxA << ", " << segIdxB << endl
<< "\tDidn't intersect" << endl;
throw runtime_error("failed");
}
}
segIdxA.Set( 0, 5.5, 5.5 );
segIdxB.Set( 4, 5.5, 5.5 );
VectorOps::IntersectionResult rInt =
vol->VoxelIntersectsSegment( idx, segIdxA, segIdxB, intIdx );
if ( VectorOps::dontIntersect != rInt ) {
cerr << "Failed VoxelIntersectsSegment test: idx " << idx
<< ", seg " << segIdxA << ", " << segIdxB << endl
<< "\tIntersected" << endl;
throw runtime_error("failed");
}
}
// FindRASPointsOnSegment
{
}
// GetVoxelsWithValue
{
// This is a 5cubed volume whose values are set to the x
// coordinate. So for x=3,y=0..4,z=0..4, value = 3.
string fnVol = "test_data/testVolumeCollection-GetVoxelsWithValue.mgh";
ifstream fVol( fnMRI.c_str(), ios::in );
if ( !fVol ) {
throw runtime_error("Couldn't find necessary test data.");
}
fVol.close();
VolumeCollection* vol = new VolumeCollection();
vol->SetFileName( fnVol );
vol->LoadVolume();
// Get the values 0-4 and make sure we got the right voxels.
for ( int nStructure = 0; nStructure < 5; nStructure++ ) {
list<VolumeLocation> lLocations;
vol->GetVoxelsWithValue( nStructure, lLocations );
Volume3<bool> bGot( 5, 5, 5, false );
list<VolumeLocation>::iterator tLocation;
for ( tLocation = lLocations.begin(); tLocation != lLocations.end();
++tLocation ) {
VolumeLocation loc = *(tLocation);
bGot.Set( loc.Index()[0], loc.Index()[1], loc.Index()[2], true );
}
for ( int nZ = 0; nZ < 5; nZ++ ) {
for ( int nY = 0; nY < 5; nY++ ) {
for ( int nX = 0; nX < 5; nX++ ) {
if ( nX == nStructure && !bGot.Get( nX, nY, nZ ) ) {
stringstream ssErr;
ssErr << "Failed GetVoxelsWithValue test: "
<< " nStructure = " << nStructure
<< " index " << Point3<int>(nX,nY,nZ)
<< " - was supposed to get voxel but didn't";
throw runtime_error(ssErr.str());
}
if ( nX != nStructure && bGot.Get( nX, nY, nZ ) ) {
stringstream ssErr;
ssErr << "Failed GetVoxelsWithValue test: "
<< " nStructure = " << nStructure
<< " index " << Point3<int>(nX,nY,nZ)
<< " - wasn't supposed to get voxel but did";
throw runtime_error(ssErr.str());
}
}
}
}
}
delete vol;
}
// GetAverageValue
{
// We'll use the same volume as with GetVoxelsWithValue.
string fnVol = "test_data/testVolumeCollection-GetVoxelsWithValue.mgh";
ifstream fVol( fnMRI.c_str(), ios::in );
if ( !fVol ) {
throw runtime_error("Couldn't find necessary test data.");
}
fVol.close();
VolumeCollection* vol = new VolumeCollection();
vol->SetFileName( fnVol );
vol->LoadVolume();
// Get values of all voxels in plane x=3 and make sure it's 3.
list<VolumeLocation> lVoxels;
for ( int nZ = 0; nZ < 5; nZ++ ) {
for ( int nY = 0; nY < 5; nY++ ) {
int index[3] = { 3, nY, nZ };
VolumeLocation loc( vol->MakeVolumeLocationFromIndex( index ) );
lVoxels.push_back( loc );
}
}
float average = vol->GetAverageValue( lVoxels );
if ( average != 3.0 ) {
stringstream ssErr;
ssErr << "Failed GetAverageValue: Getting all voxels in x=3, "
<< "average should have been 3, but was " << average;
throw runtime_error( ssErr.str() );
}
// Get values of 5 voxels, one from each x plane
// (val=0,1,2,3,4), and make sure it's 2.
lVoxels.clear();
for ( int nX = 0; nX < 5; nX++ ) {
int index[3] = { nX, 3, 3 };
VolumeLocation loc( vol->MakeVolumeLocationFromIndex( index ) );
lVoxels.push_back( loc );
}
average = vol->GetAverageValue( lVoxels );
if ( average != 2.0 ) {
stringstream ssErr;
ssErr << "Failed GetAverageValue: Getting voxels in different planes, "
<< "average should have been 2, but was " << average;
throw runtime_error( ssErr.str() );
}
// Make sure we get an error for no voxels.
lVoxels.clear();
bool bDidntThrow = false;
try {
average = vol->GetAverageValue( lVoxels );
bDidntThrow = true;
} catch ( exception& e ) {}
if ( bDidntThrow ) {
stringstream ssErr;
ssErr << "Failed GetAverageValue: Didn't throw with empty list";
throw runtime_error( ssErr.str() );
}
delete vol;
}
// Check the tcl commands.
char sCommand[1024];
int rTcl;
int id = vol->GetID();
string fnTest = "test-name";
sprintf( sCommand, "SetVolumeCollectionFileName %d test-name", id );
rTcl = Tcl_Eval( iInterp, sCommand );
AssertTclOK( rTcl );
Assert( (vol->mfnMRI == fnTest),
"Setting file name via tcl didn't work" );
vol->SetDataToWorldTransform( 0 );
delete vol;
delete testVol;
} catch ( exception& e ) {
cerr << "failed with exception: " << e.what() << endl;
exit( 1 );
} catch (...) {
cerr << "failed." << endl;
exit( 1 );
}
}