/*
* R_FreeCinematic
*/
void R_FreeCinematic( unsigned int id )
{
r_cinhandle_t *handle;
handle = R_GetCinematicHandleById( id );
if( !handle ) {
return;
}
ri.CIN_Close( handle->cin );
handle->cin = NULL;
assert( handle->name );
R_Free( handle->name );
handle->name = NULL;
assert( handle->uploadName );
R_Free( handle->uploadName );
handle->uploadName = NULL;
// remove from linked active list
handle->prev->next = handle->next;
handle->next->prev = handle->prev;
// insert into linked free list
handle->next = r_free_cinematics;
r_free_cinematics = handle;
}
/*
* SkinFile_FreeSkinFile
*/
static void SkinFile_FreeSkinFile( skinfile_t *skinfile ) {
int i;
if( skinfile->numpairs ) {
for( i = 0; i < skinfile->numpairs; i++ )
R_Free( skinfile->pairs[i].meshname );
R_Free( skinfile->pairs );
}
R_Free( skinfile->name );
memset( skinfile, 0, sizeof( skinfile_t ) );
}
/*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
permuto will return a vector of all permutations needed for bruvo's distance.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
SEXP permuto(SEXP perm)
{
int permutations;
int i;
int per;
SEXP Rval;
/*
IMPORTANT: INITIALIZE THE COUNTER. THE POINTER IS NOT RELEASED FROM
MEMORY OTHERWISE.
*/
perm_count = 0;
perm = coerceVector(perm, INTSXP);
per = INTEGER(perm)[0];
int *allele_array;
allele_array = R_Calloc(per, int);
permutations = fact(per)*per;
for(i = 0; i < per; i++)
{
allele_array[i] = i;
}
PROTECT(Rval = allocVector(INTSXP, permutations));
permute(allele_array, 0, per-1, INTEGER(Rval));
UNPROTECT(1);
R_Free(allele_array);
return Rval;
}
SEXP dotask(SEXP Sclient, SEXP Sfun, SEXP Swork, SEXP Suval, SEXP Sback, SEXP Shigh){
rgearman_client_t *client = (rgearman_client_t *)R_ExternalPtrAddr(Sclient);
SEXP ret;
const char *fun, *work, *uval;
int back, high;
fun = (Sfun != R_NilValue)? (const char *)CHAR(STRING_ELT(Sfun,0)) : NULL;
work = (Swork != R_NilValue)? (const char *)CHAR(STRING_ELT(Swork,0)) : NULL;
uval = (Suval != R_NilValue)? (const char *)CHAR(STRING_ELT(Suval,0)) : NULL;
back = LOGICAL(Sback)[0];
high = (Shigh != R_NilValue) ? LOGICAL(Shigh)[0] : -1;
if (back){
gearman_return_t (*gm_fun)(gearman_client_st *client, const char *function_name, const char *unique, const void *workload, size_t workload_size, gearman_job_handle_t job_handle);
char *job = (char *)R_Calloc(1,gearman_job_handle_t);
gm_fun = (high == -1)? gearman_client_do_background : (high)? gearman_client_do_high_background : gearman_client_do_low_background ;
client->lastretcode = gm_fun(client->client,fun,uval,work,strlen(work),job);
ret = PROTECT(allocVector(STRSXP,1));
SET_STRING_ELT(ret,0,mkChar(job));
R_Free(job);
UNPROTECT(1);
} else {
void *(*gm_fun)(gearman_client_st *client, const char *function_name, const char *unique, const void *workload, size_t workload_size, size_t *result_size, gearman_return_t *ret_ptr);
size_t resultsize;
void *result;
gm_fun = (high == -1)? gearman_client_do : (high)? gearman_client_do_high : gearman_client_do_low ;
result = gm_fun(client->client,fun,uval,work,strlen(work),&resultsize,&client->lastretcode);
ret = PROTECT(allocVector(STRSXP,1));
SET_STRING_ELT(ret,0,mkCharLen((char *)result,resultsize));
UNPROTECT(1);
}
return ret;
}
qboolean RE_RegisterModels_LevelLoadEnd(qboolean bDeleteEverythingNotUsedThisLevel /* = qfalse */)
{
qboolean bAtLeastoneModelFreed = qfalse;
if (gbInsideRegisterModel)
{
Com_DPrintf( "(Inside RE_RegisterModel (z_malloc recovery?), exiting...\n");
}
else
{
int iLoadedModelBytes = GetModelDataAllocSize();
const int iMaxModelBytes= r_modelpoolmegs->integer * 1024 * 1024;
for (CachedModels_t::iterator itModel = CachedModels->begin(); itModel != CachedModels->end() && ( bDeleteEverythingNotUsedThisLevel || iLoadedModelBytes > iMaxModelBytes ); )
{
CachedEndianedModelBinary_t &CachedModel = (*itModel).second;
qboolean bDeleteThis = qfalse;
if (bDeleteEverythingNotUsedThisLevel)
{
bDeleteThis = (qboolean)(CachedModel.iLastLevelUsedOn != RE_RegisterMedia_GetLevel());
}
else
{
bDeleteThis = (qboolean)(CachedModel.iLastLevelUsedOn < RE_RegisterMedia_GetLevel());
}
// if it wasn't used on this level, dump it...
//
if (bDeleteThis)
{
#ifdef _DEBUG
// LPCSTR psModelName = (*itModel).first.c_str();
// ri.Printf( PRINT_DEVELOPER, "Dumping \"%s\"", psModelName);
// ri.Printf( PRINT_DEVELOPER, ", used on lvl %d\n",CachedModel.iLastLevelUsedOn);
#endif
if (CachedModel.pModelDiskImage) {
R_Free(CachedModel.pModelDiskImage);
//CachedModel.pModelDiskImage = NULL; // REM for reference, erase() call below negates the need for it.
bAtLeastoneModelFreed = qtrue;
}
CachedModels->erase(itModel++);
iLoadedModelBytes = GetModelDataAllocSize();
}
else
{
++itModel;
}
}
}
//ri.Printf( PRINT_DEVELOPER, "RE_RegisterModels_LevelLoadEnd(): Ok\n");
return bAtLeastoneModelFreed;
}
// only called from devmapbsp, devmapall, or ...
//
void RE_AnimationCFGs_DeleteAll(void)
{
for (AnimationCFGs_t::iterator it = AnimationCFGs.begin(); it != AnimationCFGs.end(); ++it)
{
char *psText = (*it).second;
R_Free(psText);
}
AnimationCFGs.clear();
}
/*
* R_VBOElemBuffer
*/
static elem_t *R_VBOElemBuffer( unsigned numElems )
{
if( numElems > r_vbo_numtempelems ) {
if( r_vbo_numtempelems )
R_Free( r_vbo_tempelems );
r_vbo_numtempelems = numElems;
r_vbo_tempelems = ( elem_t * )R_Malloc( sizeof( *r_vbo_tempelems ) * numElems );
}
return r_vbo_tempelems;
}
/*
* R_VBOVertBuffer
*/
static void *R_VBOVertBuffer( unsigned numVerts, size_t vertSize )
{
size_t size = numVerts * vertSize;
if( size > r_vbo_tempvsoupsize ) {
if( r_vbo_tempvsoup )
R_Free( r_vbo_tempvsoup );
r_vbo_tempvsoupsize = size;
r_vbo_tempvsoup = ( float * )R_Malloc( size );
}
return r_vbo_tempvsoup;
}
SEXP finalizeclient(SEXP Sclient){
rgearman_client_t *client = (rgearman_client_t *)R_ExternalPtrAddr(Sclient);
if (client){
gearman_client_free(client->client);
R_Free(client);
} else
warning("GearmanClient::finalize called with NULL client");
return R_NilValue;
}
/*
* R_ShutdownCinematics
*/
void R_ShutdownCinematics( void ) {
r_cinhandle_t *handle, *hnode, *next;
hnode = &r_cinematics_headnode;
for( handle = hnode->prev; handle != hnode; handle = next ) {
next = handle->prev;
R_FreeCinematic( handle->id );
}
R_Free( r_cinematics );
}
// Compute Euclidean (L2)/Manhattan (L1) distance map of matrix _a
// Input: numeric matrix _a, of size width*height, where 0 is background and everything else is foreground. _a shouldn't contain any NAs
// Input: integer _metric. If 0, will compute Euclidean distance and Manhattan distance otherwise
// Output: distance matrix of same size as _a
SEXP distmap(SEXP _a, SEXP _metric) {
SEXP res;
int i,nprotect=0,nz;
// check validity
validImage(_a,0);
// initialize width, height, dim
width=INTEGER(GET_DIM(_a))[0];
height=INTEGER(GET_DIM(_a))[1];
nz=getNumberOfFrames(_a,0);
// initialize vj, where (i,vj[i]) are the coordinates of the closest background pixel to a(i,j) with vj[i]>=j
vj=(int *)R_Calloc(height,int);
// initialize d, the output distance matrix
PROTECT(res = allocVector(REALSXP, XLENGTH(_a)) );
nprotect++;
DUPLICATE_ATTRIB(res, _a);
d=REAL(res);
for (i=0;i<height*width*nz;i++) d[i]=R_PosInf;
// initialize dist, the distance type
metric=INTEGER(_metric)[0];
// do the job
int sizexy = height*width;
int offset = 0;
for (i=0; i<nz; i++, offset+=sizexy) {
d = &(REAL(res)[offset]);
switch (TYPEOF(_a)) {
case LGLSXP:
case INTSXP:
_distmap<int>( &(INTEGER(_a)[offset]) );
break;
case REALSXP:
_distmap<double>( &(REAL(_a)[offset]) );
break;
}
}
// final square root for Euclidean distance
d=REAL(res);
if (metric==0) for (i=0;i<height*width*nz;i++) d[i]=sqrt(d[i]);
R_Free(vj);
UNPROTECT (nprotect);
return res;
}
void RE_SaveJPG(const char * filename, int quality, int image_width, int image_height, byte *image_buffer, int padding)
{
byte *out;
size_t bufSize;
bufSize = image_width * image_height * 3;
out = (byte *) R_Malloc( bufSize, TAG_TEMP_WORKSPACE, qfalse );
bufSize = RE_SaveJPGToBuffer(out, bufSize, quality, image_width, image_height, image_buffer, padding, false);
ri.FS_WriteFile(filename, out, bufSize);
R_Free(out);
}
/*
* R_FreeCinematic
*/
void R_FreeCinematic( unsigned int id ) {
qmutex_t *lock;
r_cinhandle_t *handle;
handle = R_GetCinematicHandleById( id );
if( !handle ) {
return;
}
lock = handle->lock;
ri.Mutex_Lock( lock );
ri.CIN_Close( handle->cin );
handle->cin = NULL;
handle->lock = NULL;
assert( handle->name );
R_Free( handle->name );
handle->name = NULL;
assert( handle->uploadName );
R_Free( handle->uploadName );
handle->uploadName = NULL;
// remove from linked active list
handle->prev->next = handle->next;
handle->next->prev = handle->prev;
// insert into linked free list
handle->next = r_free_cinematics;
r_free_cinematics = handle;
ri.Mutex_Unlock( lock );
ri.Mutex_Destroy( &lock );
}
/*
================
R_MipMap2
Uses temp mem, but then copies back to input, quartering the size of the texture
Proper linear filter
================
*/
static void R_MipMap2( unsigned *in, int inWidth, int inHeight ) {
int i, j, k;
byte *outpix;
int inWidthMask, inHeightMask;
int total;
int outWidth, outHeight;
unsigned *temp;
outWidth = inWidth >> 1;
outHeight = inHeight >> 1;
temp = (unsigned int *) R_Malloc( outWidth * outHeight * 4, TAG_TEMP_WORKSPACE, qfalse );
inWidthMask = inWidth - 1;
inHeightMask = inHeight - 1;
for ( i = 0 ; i < outHeight ; i++ ) {
for ( j = 0 ; j < outWidth ; j++ ) {
outpix = (byte *) ( temp + i * outWidth + j );
for ( k = 0 ; k < 4 ; k++ ) {
total =
1 * ((byte *)&in[ ((i*2-1)&inHeightMask)*inWidth + ((j*2-1)&inWidthMask) ])[k] +
2 * ((byte *)&in[ ((i*2-1)&inHeightMask)*inWidth + ((j*2)&inWidthMask) ])[k] +
2 * ((byte *)&in[ ((i*2-1)&inHeightMask)*inWidth + ((j*2+1)&inWidthMask) ])[k] +
1 * ((byte *)&in[ ((i*2-1)&inHeightMask)*inWidth + ((j*2+2)&inWidthMask) ])[k] +
2 * ((byte *)&in[ ((i*2)&inHeightMask)*inWidth + ((j*2-1)&inWidthMask) ])[k] +
4 * ((byte *)&in[ ((i*2)&inHeightMask)*inWidth + ((j*2)&inWidthMask) ])[k] +
4 * ((byte *)&in[ ((i*2)&inHeightMask)*inWidth + ((j*2+1)&inWidthMask) ])[k] +
2 * ((byte *)&in[ ((i*2)&inHeightMask)*inWidth + ((j*2+2)&inWidthMask) ])[k] +
2 * ((byte *)&in[ ((i*2+1)&inHeightMask)*inWidth + ((j*2-1)&inWidthMask) ])[k] +
4 * ((byte *)&in[ ((i*2+1)&inHeightMask)*inWidth + ((j*2)&inWidthMask) ])[k] +
4 * ((byte *)&in[ ((i*2+1)&inHeightMask)*inWidth + ((j*2+1)&inWidthMask) ])[k] +
2 * ((byte *)&in[ ((i*2+1)&inHeightMask)*inWidth + ((j*2+2)&inWidthMask) ])[k] +
1 * ((byte *)&in[ ((i*2+2)&inHeightMask)*inWidth + ((j*2-1)&inWidthMask) ])[k] +
2 * ((byte *)&in[ ((i*2+2)&inHeightMask)*inWidth + ((j*2)&inWidthMask) ])[k] +
2 * ((byte *)&in[ ((i*2+2)&inHeightMask)*inWidth + ((j*2+1)&inWidthMask) ])[k] +
1 * ((byte *)&in[ ((i*2+2)&inHeightMask)*inWidth + ((j*2+2)&inWidthMask) ])[k];
outpix[k] = total / 36;
}
}
}
memcpy( in, temp, outWidth * outHeight * 4 );
R_Free( temp );
}
// Compute Euclidean (L2)/Manhattan (L1) distance map of matrix _a
// Input: numeric matrix _a, of size width*height, where 0 is background and everything else is foreground. _a shouldn't contain any NAs
// Input: integer _metric. If 0, will compute Euclidean distance and Manhattan distance otherwise
// Output: distance matrix of same size as _a
SEXP distmap(SEXP _a, SEXP _metric) {
SEXP res;
int i,nprotect=0,nz;
// check validity
validImage(_a,0);
// initialize width, height, dim
width=INTEGER(GET_DIM(_a))[0];
height=INTEGER(GET_DIM(_a))[1];
nz=getNumberOfFrames(_a,0);
// initialize vj, where (i,vj[i]) are the coordinates of the closest background pixel to a(i,j) with vj[i]>=j
vj=(int *)R_Calloc(height,int);
// initialize a
a=REAL(_a);
// initialize d, the output distance matrix
PROTECT(res=Rf_duplicate(_a));
nprotect++;
d=REAL(res);
for (i=0;i<height*width*nz;i++) d[i]=R_PosInf;
// initialize dist, the distance type
metric=INTEGER(_metric)[0];
// do the job
for (i=0;i<nz;i++) {
distmap_onesided(1);
distmap_onesided(0);
a=a+height*width;
d=d+height*width;
}
// final square root for Euclidean distance
d=REAL(res);
if (metric==0) for (i=0;i<height*width*nz;i++) d[i]=sqrt(d[i]);
// free vj
R_Free(vj);
UNPROTECT (nprotect);
return res;
}
/*
* R_ReserveDrawSurfaces
*/
static void R_ReserveDrawSurfaces( drawList_t *list, int minMeshes )
{
int oldSize, newSize;
sortedDrawSurf_t *newDs;
sortedDrawSurf_t *ds = list->drawSurfs;
int maxMeshes = list->maxDrawSurfs;
oldSize = maxMeshes;
newSize = max( minMeshes, oldSize * 2 );
newDs = R_Malloc( newSize * sizeof( sortedDrawSurf_t ) );
if( ds ) {
memcpy( newDs, ds, oldSize * sizeof( sortedDrawSurf_t ) );
R_Free( ds );
}
list->drawSurfs = newDs;
list->maxDrawSurfs = newSize;
}
static void RE_RegisterModels_DeleteAll(void)
{
if(!CachedModels) {
return; //argh!
}
for (CachedModels_t::iterator itModel = CachedModels->begin(); itModel != CachedModels->end(); )
{
CachedEndianedModelBinary_t &CachedModel = (*itModel).second;
if (CachedModel.pModelDiskImage) {
R_Free(CachedModel.pModelDiskImage);
}
CachedModels->erase(itModel++);
}
extern void RE_AnimationCFGs_DeleteAll(void);
RE_AnimationCFGs_DeleteAll();
}
/*
* R_ShutdownVBO
*/
void R_ShutdownVBO( void )
{
mesh_vbo_t *vbo;
vbohandle_t *vboh, *next, *hnode;
if( !r_num_active_vbos ) {
return;
}
hnode = &r_vbohandles_headnode;
for( vboh = hnode->prev; vboh != hnode; vboh = next ) {
next = vboh->prev;
vbo = &r_mesh_vbo[vboh->index];
R_ReleaseMeshVBO( vbo );
}
if( r_vbo_tempelems ) {
R_Free( r_vbo_tempelems );
}
r_vbo_numtempelems = 0;
}
void do_free(SEXP x)
{
void* addr = R_ExternalPtrAddr(x);
R_Free(addr);
}
SEXP clahe (SEXP x, SEXP _uiNrX, SEXP _uiNrY, SEXP _uiNrBins, SEXP _fCliplimit, SEXP _keepRange) {
int nx, ny, nz, i, j;
unsigned int uiNrX, uiNrY, uiNrBins;
float fCliplimit;
int keepRange;
double *src, *tgt;
SEXP res;
kz_pixel_t min = 0, max = uiNR_OF_GREY-1;
kz_pixel_t *img;
double maxPixelValue = uiNR_OF_GREY-1;
PROTECT( res = allocVector(REALSXP, XLENGTH(x)) );
DUPLICATE_ATTRIB(res, x);
nx = INTEGER(GET_DIM(x))[0];
ny = INTEGER(GET_DIM(x))[1];
nz = getNumberOfFrames(x, 0);
uiNrX = INTEGER(_uiNrX)[0];
uiNrY = INTEGER(_uiNrY)[0];
uiNrBins = INTEGER(_uiNrBins)[0];
fCliplimit = REAL(_fCliplimit)[0];
keepRange = LOGICAL(_keepRange)[0];
img = R_Calloc(nx*ny, kz_pixel_t);
// process channels separately
for(j = 0; j < nz; j++) {
src = &(REAL(x)[j*nx*ny]);
tgt = &(REAL(res)[j*nx*ny]);
if (keepRange) {
min = uiNR_OF_GREY-1;
max = 0;
}
// convert frame to CLAHE-compatible format
for (i = 0; i < nx*ny; i++) {
double el = src[i];
// clip
if (el < 0.0) el = 0;
else if (el > 1.0) el = 1.0;
// convert to int
kz_pixel_t nel = (kz_pixel_t) round(el * maxPixelValue);
if (keepRange) {
if (nel < min) min = nel;
if (nel > max) max = nel;
}
img[i] = nel;
}
int val = CLAHE (img, (unsigned int) nx, (unsigned int) ny,
min, max, uiNrX, uiNrY, uiNrBins, fCliplimit);
// translate internal error codes
switch (val) {
case -1:
error("# of regions x-direction too large");
break;
case -2:
error("# of regions y-direction too large");
break;
case -3:
error("x-resolution no multiple of 'nx'");
break;
case -4:
error("y-resolution no multiple of 'ny'");
break;
case -5:
error("maximum too large");
break;
case -6:
error("minimum equal or larger than maximum");
break;
case -7:
error("at least 4 contextual regions required");
break;
case -8:
error("not enough memory! (try reducing 'bins')");
break;
}
// convert back to [0:1] range
for (i = 0; i < nx*ny; i++) {
tgt[i] = (double) img[i] / maxPixelValue;
}
}
R_Free(img);
UNPROTECT(1);
return res;
}
/*
* Mod_LoadSkeletalModel
*/
void Mod_LoadSkeletalModel( model_t *mod, const model_t *parent, void *buffer, bspFormatDesc_t *unused )
{
unsigned int i, j, k;
size_t filesize;
qbyte *pbase;
size_t memsize;
qbyte *pmem;
iqmheader_t *header;
char *texts;
iqmvertexarray_t *va;
iqmjoint_t *joints;
bonepose_t *baseposes;
iqmpose_t *poses;
unsigned short *framedata;
const int *inelems;
elem_t *outelems;
iqmmesh_t *inmesh;
iqmbounds_t *inbounds;
float *vposition, *vtexcoord, *vnormal, *vtangent;
qbyte *vblendindices_byte, *vblendweights_byte;
int *vblendindexes_int;
float *vblendweights_float;
mskmodel_t *poutmodel;
baseposes = NULL;
header = ( iqmheader_t * )buffer;
// check IQM magic
if( memcmp( header->magic, "INTERQUAKEMODEL", 16 ) ) {
ri.Com_Printf( S_COLOR_RED "ERROR: %s is not an Inter-Quake Model\n", mod->name );
goto error;
}
// check header version
header->version = LittleLong( header->version );
if( header->version != IQM_VERSION ) {
ri.Com_Printf( S_COLOR_RED "ERROR: %s has wrong type number (%i should be %i)\n", mod->name, header->version, IQM_VERSION );
goto error;
}
// byteswap header
#define H_SWAP(s) (header->s = LittleLong( header->s ))
H_SWAP( filesize );
H_SWAP( flags );
H_SWAP( num_text );
H_SWAP( ofs_text );
H_SWAP( num_meshes );
H_SWAP( ofs_meshes );
H_SWAP( num_vertexarrays );
H_SWAP( num_vertexes );
H_SWAP( ofs_vertexarrays );
H_SWAP( num_triangles );
H_SWAP( ofs_triangles );
H_SWAP( ofs_adjacency );
H_SWAP( num_joints );
H_SWAP( ofs_joints );
H_SWAP( num_poses );
H_SWAP( ofs_poses );
H_SWAP( num_anims );
H_SWAP( ofs_anims );
H_SWAP( num_frames );
H_SWAP( num_framechannels );
H_SWAP( ofs_frames );
H_SWAP( ofs_bounds );
H_SWAP( num_comment );
H_SWAP( ofs_comment );
H_SWAP( num_extensions );
H_SWAP( ofs_extensions );
#undef H_SWAP
if( header->num_triangles < 1 || header->num_vertexes < 3 || header->num_vertexarrays < 1 || header->num_meshes < 1 ) {
ri.Com_Printf( S_COLOR_RED "ERROR: %s has no geometry\n", mod->name );
goto error;
}
if( header->num_frames < 1 || header->num_anims < 1 ) {
ri.Com_Printf( S_COLOR_RED "ERROR: %s has no animations\n", mod->name );
goto error;
}
if( header->num_joints != header->num_poses ) {
ri.Com_Printf( S_COLOR_RED "ERROR: %s has an invalid number of poses: %i vs %i\n", mod->name, header->num_joints, header->num_poses );
goto error;
}
if( !header->ofs_bounds ) {
ri.Com_Printf( S_COLOR_RED "ERROR: %s has no frame bounds\n", mod->name );
goto error;
}
pbase = ( qbyte * )buffer;
filesize = header->filesize;
// check data offsets against the filesize
if( header->ofs_text + header->num_text > filesize
|| header->ofs_vertexarrays + header->num_vertexarrays * sizeof( iqmvertexarray_t ) > filesize
|| header->ofs_joints + header->num_joints * sizeof( iqmjoint_t ) > filesize
|| header->ofs_frames + header->num_frames * header->num_framechannels * sizeof( unsigned short ) > filesize
|| header->ofs_triangles + header->num_triangles * sizeof( int[3] ) > filesize
|| header->ofs_meshes + header->num_meshes * sizeof( iqmmesh_t ) > filesize
|| header->ofs_bounds + header->num_frames * sizeof( iqmbounds_t ) > filesize
) {
ri.Com_Printf( S_COLOR_RED "ERROR: %s has invalid size or offset information\n", mod->name );
goto error;
}
poutmodel = mod->extradata = Mod_Malloc( mod, sizeof( *poutmodel ) );
// load text
texts = Mod_Malloc( mod, header->num_text + 1 );
if( header->ofs_text ) {
memcpy( texts, (const char *)(pbase + header->ofs_text), header->num_text );
}
texts[header->ofs_text] = '\0';
// load vertex arrays
vposition = NULL;
vtexcoord = NULL;
vnormal = NULL;
vtangent = NULL;
vblendindices_byte = NULL;
vblendindexes_int = NULL;
vblendweights_byte = NULL;
vblendweights_float = NULL;
va = ( iqmvertexarray_t * )( pbase + header->ofs_vertexarrays );
for( i = 0; i < header->num_vertexarrays; i++ ) {
size_t vsize;
va[i].type = LittleLong( va[i].type );
va[i].flags = LittleLong( va[i].flags );
va[i].format = LittleLong( va[i].format );
va[i].size = LittleLong( va[i].size );
va[i].offset = LittleLong( va[i].offset );
vsize = header->num_vertexes*va[i].size;
switch( va[i].format ) {
case IQM_FLOAT:
vsize *= sizeof( float );
break;
case IQM_INT:
case IQM_UINT:
vsize *= sizeof( int );
break;
case IQM_BYTE:
case IQM_UBYTE:
vsize *= sizeof( unsigned char );
break;
default:
continue;
}
if( va[i].offset + vsize > filesize ) {
continue;
}
switch( va[i].type ) {
case IQM_POSITION:
if( va[i].format == IQM_FLOAT && va[i].size == 3 ) {
vposition = ( float * )( pbase + va[i].offset );
}
break;
case IQM_TEXCOORD:
if( va[i].format == IQM_FLOAT && va[i].size == 2 ) {
vtexcoord = ( float * )( pbase + va[i].offset );
}
break;
case IQM_NORMAL:
if( va[i].format == IQM_FLOAT && va[i].size == 3 ) {
vnormal = ( float * )( pbase + va[i].offset );
}
break;
case IQM_TANGENT:
if( va[i].format == IQM_FLOAT && va[i].size == 4 ) {
vtangent = ( float * )( pbase + va[i].offset );
}
break;
case IQM_BLENDINDEXES:
if( va[i].size != SKM_MAX_WEIGHTS )
break;
if( va[i].format == IQM_BYTE || va[i].format == IQM_UBYTE ) {
vblendindices_byte = ( qbyte * )( pbase + va[i].offset );
}
else if( va[i].format == IQM_INT || va[i].format == IQM_UINT ) {
vblendindexes_int = ( int * )( pbase + va[i].offset );
}
break;
case IQM_BLENDWEIGHTS:
if( va[i].size != SKM_MAX_WEIGHTS )
break;
if( va[i].format == IQM_UBYTE ) {
vblendweights_byte = ( qbyte * )( pbase + va[i].offset );
}
else if( va[i].format == IQM_FLOAT ) {
vblendweights_float = ( float * )( pbase + va[i].offset );
}
break;
default:
break;
}
}
if( !vposition || !vtexcoord
|| !(vblendindices_byte || vblendindexes_int)
|| !(vblendweights_byte || vblendweights_float) ) {
ri.Com_Printf( S_COLOR_RED "ERROR: %s is missing vertex array data\n", mod->name );
goto error;
}
// load joints
memsize = 0;
memsize += sizeof( bonepose_t ) * header->num_joints;
pmem = Mod_Malloc( mod, memsize );
baseposes = ( void * )pmem; pmem += sizeof( *baseposes );
memsize = 0;
memsize += sizeof( mskbone_t ) * header->num_joints;
memsize += sizeof( bonepose_t ) * header->num_joints;
pmem = Mod_Malloc( mod, memsize );
poutmodel->numbones = header->num_joints;
poutmodel->bones = ( void * )pmem; pmem += sizeof( *poutmodel->bones ) * poutmodel->numbones;
poutmodel->invbaseposes = ( void * )pmem; pmem += sizeof( *poutmodel->invbaseposes ) * poutmodel->numbones;
joints = ( iqmjoint_t * )( pbase + header->ofs_joints );
for( i = 0; i < poutmodel->numbones; i++ ) {
joints[i].name = LittleLong( joints[i].name );
joints[i].parent = LittleLong( joints[i].parent );
for( j = 0; j < 3; j++ ) {
joints[i].translate[j] = LittleFloat( joints[i].translate[j] );
joints[i].rotate[j] = LittleFloat( joints[i].rotate[j] );
joints[i].scale[j] = LittleFloat( joints[i].scale[j] );
}
if( joints[i].parent >= (int)i ) {
ri.Com_Printf( S_COLOR_RED "ERROR: %s bone[%i].parent(%i) >= %i\n", mod->name, i, joints[i].parent, i );
goto error;
}
poutmodel->bones[i].name = texts + joints[i].name;
poutmodel->bones[i].parent = joints[i].parent;
DualQuat_FromQuat3AndVector( joints[i].rotate, joints[i].translate, baseposes[i].dualquat );
// scale is unused
// reconstruct invserse bone pose
if( joints[i].parent >= 0 )
{
bonepose_t bp, *pbp;
bp = baseposes[i];
pbp = &baseposes[joints[i].parent];
DualQuat_Multiply( pbp->dualquat, bp.dualquat, baseposes[i].dualquat );
}
DualQuat_Copy( baseposes[i].dualquat, poutmodel->invbaseposes[i].dualquat );
DualQuat_Invert( poutmodel->invbaseposes[i].dualquat );
}
// load frames
poses = ( iqmpose_t * )( pbase + header->ofs_poses );
for( i = 0; i < header->num_poses; i++ ) {
poses[i].parent = LittleLong( poses[i].parent );
poses[i].mask = LittleLong( poses[i].mask );
for( j = 0; j < 10; j++ ) {
poses[i].channeloffset[j] = LittleFloat( poses[i].channeloffset[j] );
poses[i].channelscale[j] = LittleFloat( poses[i].channelscale[j] );
}
}
memsize = 0;
memsize += sizeof( mskframe_t ) * header->num_frames;
memsize += sizeof( bonepose_t ) * header->num_joints * header->num_frames;
pmem = Mod_Malloc( mod, memsize );
poutmodel->numframes = header->num_frames;
poutmodel->frames = ( mskframe_t * )pmem; pmem += sizeof( mskframe_t ) * poutmodel->numframes;
framedata = ( unsigned short * )( pbase + header->ofs_frames );
for( i = 0; i < header->num_frames; i++ ) {
bonepose_t *pbp;
vec3_t translate;
quat_t rotate;
poutmodel->frames[i].boneposes = ( bonepose_t * )pmem; pmem += sizeof( bonepose_t ) * poutmodel->numbones;
for( j = 0, pbp = poutmodel->frames[i].boneposes; j < header->num_poses; j++, pbp++ ) {
translate[0] = poses[j].channeloffset[0]; if( poses[j].mask & 0x01 ) translate[0] += *framedata++ * poses[j].channelscale[0];
translate[1] = poses[j].channeloffset[1]; if( poses[j].mask & 0x02 ) translate[1] += *framedata++ * poses[j].channelscale[1];
translate[2] = poses[j].channeloffset[2]; if( poses[j].mask & 0x04 ) translate[2] += *framedata++ * poses[j].channelscale[2];
rotate[0] = poses[j].channeloffset[3]; if( poses[j].mask & 0x08 ) rotate[0] += *framedata++ * poses[j].channelscale[3];
rotate[1] = poses[j].channeloffset[4]; if( poses[j].mask & 0x10 ) rotate[1] += *framedata++ * poses[j].channelscale[4];
rotate[2] = poses[j].channeloffset[5]; if( poses[j].mask & 0x20 ) rotate[2] += *framedata++ * poses[j].channelscale[5];
rotate[3] = poses[j].channeloffset[6]; if( poses[j].mask & 0x40 ) rotate[3] += *framedata++ * poses[j].channelscale[6];
if( rotate[3] > 0 ) {
Vector4Inverse( rotate );
}
Vector4Normalize( rotate );
// scale is unused
if( poses[j].mask & 0x80 ) framedata++;
if( poses[j].mask & 0x100 ) framedata++;
if( poses[j].mask & 0x200 ) framedata++;
DualQuat_FromQuatAndVector( rotate, translate, pbp->dualquat );
}
}
// load triangles
memsize = 0;
memsize += sizeof( *outelems ) * header->num_triangles * 3;
pmem = Mod_Malloc( mod, memsize );
poutmodel->numtris = header->num_triangles;
poutmodel->elems = ( elem_t * )pmem; pmem += sizeof( *outelems ) * header->num_triangles * 3;
inelems = ( const int * )(pbase + header->ofs_triangles);
outelems = poutmodel->elems;
for( i = 0; i < header->num_triangles; i++ ) {
for( j = 0; j < 3; j++ ) {
outelems[j] = LittleLong( inelems[j] );
}
inelems += 3;
outelems += 3;
}
// load vertices
memsize = 0;
memsize += sizeof( *poutmodel->sVectorsArray ) * header->num_vertexes; // 16-bytes aligned
memsize += sizeof( *poutmodel->xyzArray ) * header->num_vertexes;
memsize += sizeof( *poutmodel->normalsArray ) * header->num_vertexes;
memsize += sizeof( *poutmodel->stArray ) * header->num_vertexes;
memsize += sizeof( *poutmodel->blendWeights ) * header->num_vertexes * SKM_MAX_WEIGHTS;
memsize += sizeof( *poutmodel->blendIndices ) * header->num_vertexes * SKM_MAX_WEIGHTS;
pmem = Mod_Malloc( mod, memsize );
poutmodel->numverts = header->num_vertexes;
// S-vectors
poutmodel->sVectorsArray = ( vec4_t * )pmem; pmem += sizeof( *poutmodel->sVectorsArray ) * header->num_vertexes;
if( vtangent ) {
for( i = 0; i < header->num_vertexes; i++ ) {
for( j = 0; j < 4; j++ ) {
poutmodel->sVectorsArray[i][j] = LittleFloat( vtangent[j] );
}
vtangent += 4;
}
}
// XYZ positions
poutmodel->xyzArray = ( vec4_t * )pmem; pmem += sizeof( *poutmodel->xyzArray ) * header->num_vertexes;
for( i = 0; i < header->num_vertexes; i++ ) {
for( j = 0; j < 3; j++ ) {
poutmodel->xyzArray[i][j] = LittleFloat( vposition[j] );
}
poutmodel->xyzArray[i][3] = 1;
vposition += 3;
}
// normals
poutmodel->normalsArray = ( vec4_t * )pmem; pmem += sizeof( *poutmodel->normalsArray ) * header->num_vertexes;
for( i = 0; i < header->num_vertexes; i++ ) {
for( j = 0; j < 3; j++ ) {
poutmodel->normalsArray[i][j] = LittleFloat( vnormal[j] );
}
poutmodel->normalsArray[i][3] = 0;
vnormal += 3;
}
// texture coordinates
poutmodel->stArray = ( vec2_t * )pmem; pmem += sizeof( *poutmodel->stArray ) * header->num_vertexes;
for( i = 0; i < header->num_vertexes; i++ ) {
for( j = 0; j < 2; j++ ) {
poutmodel->stArray[i][j] = LittleFloat( vtexcoord[j] );
}
vtexcoord += 2;
}
if( !vtangent ) {
// if the loaded file is missing precomputed S-vectors, compute them now
R_BuildTangentVectors( poutmodel->numverts, poutmodel->xyzArray, poutmodel->normalsArray, poutmodel->stArray,
poutmodel->numtris, poutmodel->elems, poutmodel->sVectorsArray );
}
// blend indices
poutmodel->blendIndices = ( qbyte * )pmem; pmem += sizeof( *poutmodel->blendIndices ) * header->num_vertexes * SKM_MAX_WEIGHTS;
if( vblendindices_byte ) {
memcpy( poutmodel->blendIndices, vblendindices_byte, sizeof( qbyte ) * header->num_vertexes * SKM_MAX_WEIGHTS );
} else if( vblendindexes_int ) {
for( j = 0; j < header->num_vertexes * SKM_MAX_WEIGHTS; j++ ) {
poutmodel->blendIndices[j] = LittleLong( vblendindexes_int[j] );
}
}
// blend weights
poutmodel->blendWeights = ( qbyte * )pmem; pmem += sizeof( *poutmodel->blendWeights ) * header->num_vertexes * SKM_MAX_WEIGHTS;
if( vblendweights_byte ) {
memcpy( poutmodel->blendWeights, vblendweights_byte, sizeof( qbyte ) * header->num_vertexes * SKM_MAX_WEIGHTS );
}
else if( vblendweights_float ) {
for( j = 0; j < header->num_vertexes * SKM_MAX_WEIGHTS; j++ ) {
poutmodel->blendWeights[j] = LittleFloat( vblendweights_float[j] ) * 255.0f;
}
}
// blends
memsize = 0;
memsize += poutmodel->numverts * ( sizeof( mskblend_t ) + sizeof( unsigned int ) );
pmem = Mod_Malloc( mod, memsize );
poutmodel->numblends = 0;
poutmodel->blends = ( mskblend_t * )pmem; pmem += sizeof( *poutmodel->blends ) * poutmodel->numverts;
poutmodel->vertexBlends = ( unsigned int * )pmem;
vblendindices_byte = poutmodel->blendIndices;
vblendweights_byte = poutmodel->blendWeights;
for( i = 0; i < poutmodel->numverts; i++ ) {
mskblend_t blend;
for( j = 0; j < SKM_MAX_WEIGHTS; j++ ) {
blend.indices[j] = vblendindices_byte[j];
blend.weights[j] = vblendweights_byte[j];
}
poutmodel->vertexBlends[i] = Mod_SkeletalModel_AddBlend( poutmodel, &blend );
vblendindices_byte += SKM_MAX_WEIGHTS;
vblendweights_byte += SKM_MAX_WEIGHTS;
}
// meshes
memsize = 0;
memsize += sizeof( mskmesh_t ) * header->num_meshes;
memsize += sizeof( drawSurfaceSkeletal_t ) * header->num_meshes;
pmem = Mod_Malloc( mod, memsize );
poutmodel->nummeshes = header->num_meshes;
poutmodel->meshes = ( mskmesh_t * )pmem; pmem += sizeof( *poutmodel->meshes ) * header->num_meshes;
inmesh = ( iqmmesh_t * )(pbase + header->ofs_meshes);
for( i = 0; i < header->num_meshes; i++ ) {
inmesh[i].name = LittleLong( inmesh[i].name );
inmesh[i].material = LittleLong( inmesh[i].material );
inmesh[i].first_vertex = LittleLong( inmesh[i].first_vertex );
inmesh[i].num_vertexes = LittleLong( inmesh[i].num_vertexes );
inmesh[i].first_triangle = LittleLong( inmesh[i].first_triangle );
inmesh[i].num_triangles = LittleLong( inmesh[i].num_triangles );
poutmodel->meshes[i].name = texts + inmesh[i].name;
Mod_StripLODSuffix( poutmodel->meshes[i].name );
poutmodel->meshes[i].skin.name = texts + inmesh[i].material;
poutmodel->meshes[i].skin.shader = R_RegisterSkin( poutmodel->meshes[i].skin.name );
poutmodel->meshes[i].elems = poutmodel->elems + inmesh[i].first_triangle * 3;
poutmodel->meshes[i].numtris = inmesh[i].num_triangles;
poutmodel->meshes[i].numverts = inmesh[i].num_vertexes;
poutmodel->meshes[i].xyzArray = poutmodel->xyzArray + inmesh[i].first_vertex;
poutmodel->meshes[i].normalsArray = poutmodel->normalsArray + inmesh[i].first_vertex;
poutmodel->meshes[i].stArray = poutmodel->stArray + inmesh[i].first_vertex;
poutmodel->meshes[i].sVectorsArray = poutmodel->sVectorsArray + inmesh[i].first_vertex;
poutmodel->meshes[i].blendIndices = poutmodel->blendIndices + inmesh[i].first_vertex * SKM_MAX_WEIGHTS;
poutmodel->meshes[i].blendWeights = poutmodel->blendWeights + inmesh[i].first_vertex * SKM_MAX_WEIGHTS;
poutmodel->meshes[i].vertexBlends = poutmodel->vertexBlends + inmesh[i].first_vertex;
// elements are always offset to start vertex 0 for each mesh
outelems = poutmodel->meshes[i].elems;
for( j = 0; j < poutmodel->meshes[i].numtris; j++ ) {
outelems[0] -= inmesh[i].first_vertex;
outelems[1] -= inmesh[i].first_vertex;
outelems[2] -= inmesh[i].first_vertex;
outelems += 3;
}
poutmodel->meshes[i].maxWeights = 1;
vblendweights_byte = poutmodel->meshes[i].blendWeights;
for( j = 0; j < poutmodel->meshes[i].numverts; j++ ) {
for( k = 1; k < SKM_MAX_WEIGHTS && vblendweights_byte[k]; k++ );
if( k > poutmodel->meshes[i].maxWeights ) {
poutmodel->meshes[i].maxWeights = k;
if( k == SKM_MAX_WEIGHTS ) {
break;
}
}
vblendweights_byte += SKM_MAX_WEIGHTS;
}
// creating a VBO only makes sense if GLSL is present and the number of bones
// we can handle on the GPU is sufficient
if( glConfig.ext.vertex_buffer_object && poutmodel->numbones <= glConfig.maxGLSLBones ) {
// build a static vertex buffer object for this mesh
Mod_SkeletalBuildStaticVBOForMesh( &poutmodel->meshes[i] );
}
}
poutmodel->drawSurfs = ( drawSurfaceSkeletal_t * )pmem; pmem += sizeof( *poutmodel->drawSurfs ) * header->num_meshes;
for( i = 0; i < header->num_meshes; i++ ) {
poutmodel->drawSurfs[i].type = ST_SKELETAL;
poutmodel->drawSurfs[i].model = mod;
poutmodel->drawSurfs[i].mesh = poutmodel->meshes + i;
}
// bounds
ClearBounds( mod->mins, mod->maxs );
inbounds = ( iqmbounds_t * )(pbase + header->ofs_bounds);
for( i = 0; i < header->num_frames; i++ ) {
for( j = 0; j < 3; j++ ) {
inbounds[i].bbmin[j] = LittleFloat( inbounds[i].bbmin[j] );
inbounds[i].bbmax[j] = LittleFloat( inbounds[i].bbmax[j] );
}
inbounds[i].radius = LittleFloat( inbounds[i].radius );
inbounds[i].xyradius = LittleFloat( inbounds[i].xyradius );
VectorCopy( inbounds[i].bbmin, poutmodel->frames[i].mins );
VectorCopy( inbounds[i].bbmax, poutmodel->frames[i].maxs );
poutmodel->frames[i].radius = inbounds[i].radius;
AddPointToBounds( poutmodel->frames[i].mins, mod->mins, mod->maxs );
AddPointToBounds( poutmodel->frames[i].maxs, mod->mins, mod->maxs );
}
mod->radius = RadiusFromBounds( mod->mins, mod->maxs );
mod->type = mod_skeletal;
mod->registrationSequence = rsh.registrationSequence;
mod->touch = &Mod_TouchSkeletalModel;
R_Free( baseposes );
return;
error:
if( baseposes ) {
R_Free( baseposes );
}
mod->type = mod_bad;
}
/*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Bruvo's Distance implementing Addition, Loss, and Infinite models for
imputation of missing data.
NOTE: The input needs to be divided by the repeat length beforehand for this
to work.
in: a matrix of two individuals
out: a double value that will be the output from bruvo's distance.
n: number of individuals(2)
nall: number of alleles
perm: a vector from the permn function in R
woo: p * p!
loss: TRUE/FALSE: impute under genome loss model.
add: TRUE/FALSE: impute under genome addition model.
==============================================================================*/
double bruvo_dist(int *in, int *nall, int *perm, int *woo, int *loss, int *add, int old_model)
{
// R_CheckUserInterrupt();
int i;
int j;
int counter = 0; // counter used for building arrays
int n = 2; // number of individuals
int p = *nall; // number of alleles
int w = *woo; // number of permutations = p * p!
int loss_indicator = *loss; // 1 if the genome loss model should be used
int add_indicator = *add; // 1 if the genome addition model should be used
int* genos; // array to store the genotypes
genos = R_Calloc(2*p, int);
int zerocatch[2]; // 2 element array to store the number of missing
// alleles in each genotype.
int** zero_ind; // array to store the indices of the missing data for
// each genotype
zero_ind = R_Calloc(2, int*);
zero_ind[0] = R_Calloc(p, int);
zero_ind[1] = R_Calloc(p, int);
int zerodiff; // used to check the amount of missing data different
// between the two genotypes
double minn = 100; // The minimum distance
// reconstruct the genotype table.
zerocatch[0] = 0;
zerocatch[1] = 0;
for(i = 0; i < n; i++)
{
for(j = 0; j < p; j++)
{
// Catch missing data here.
if (in[counter] == 0)
{
if (zerocatch[i] == p - 1)
{
goto finalsteps;
}
zerocatch[i] += 1;
// Rprintf("[%d]", zerocatch[i] - 1);
zero_ind[i][zerocatch[i] - 1] = j;
}
genos[i*p + j] = in[counter++];
// Rprintf("%d\t", genos[i*p + j]);
}
// Rprintf("\n");
}
// Rprintf("\n");
zerodiff = abs(zerocatch[0] - zerocatch[1]);
/*==========================================================================
* Removing superfluous zeroes from the data. This is in the case that both
* of the genotypes contain one or more zeroes.
*
* smaller and larger refer to the size of the genotypes.
==========================================================================*/
if (zerocatch[0] > 0 && zerocatch[1] > 0)
{
int smaller = 0;
int larger = 1;
int reduction = 0;
int i;
int j;
int zero_counter;
int *perm_array;
int *new_geno;
int *new_alleles;
if (zerodiff == 0)
{
reduction = p - zerocatch[0];
}
else
{
if (zerocatch[0] < zerocatch[1])
{
smaller = 1;
larger = 0;
}
reduction = p - (zerocatch[smaller] - zerodiff);
}
new_alleles = R_Calloc(reduction, int);
for (i = 0; i < reduction; i++)
{
new_alleles[i] = i;
}
w = fact(reduction) * reduction;
perm_array = R_Calloc(w, int);
perm_count = 0;
permute(new_alleles, 0, reduction - 1, perm_array);
new_geno = R_Calloc(reduction*n, int);
counter = 0;
for (i=0; i < n; i++)
{
zero_counter = zerocatch[larger];
for (j = 0; j < p; j++)
{
if (genos[i*p + j] == 0 && zero_counter > 0)
{
zero_counter--;
}
else
{
new_geno[counter++] = genos[i*p + j];
}
}
}
minn = bruvo_dist(new_geno, &reduction, perm_array, &w,
&loss_indicator, &add_indicator, old_model);
R_Free(perm_array);
R_Free(new_geno);
R_Free(new_alleles);
goto finalsteps;
}
