void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
mxArray **analyticFnParam;
mxArray *aRandVec, *aRandVecN;
mxArray *aRandParam;
double *pRandParam, *randU, *randN;
mxArray *pointsM, *weightsM, *indicesM;
double *points, *weights;
BallTree::index* indices;
unsigned int i;
unsigned int Niter,Ndens,Ndim,Np;
/*********************************************************************
** Verify arguments and initialize variables
*********************************************************************/
if (nrhs < 3)
mexErrMsgTxt("Takes 3-5 input arguments");
if (nlhs != 2)
mexErrMsgTxt("Outputs 2 results");
Ndens = mxGetN(prhs[0]); // get # of densities
/*********************************************************************
** Transform Matlab cell arrays into struct NPD representation
*********************************************************************/
BallTreeDensity *trees = new BallTreeDensity[Ndens];
bool allGaussians = true;
for (i=0; i < Ndens; i++) {
trees[i] = BallTreeDensity( mxGetCell(prhs[0],i) );
if (trees[i].getType() != BallTreeDensity::Gaussian) allGaussians = false;
}
if (!allGaussians)
mexErrMsgTxt("Sorry -- only Gaussian kernels supported");
Ndim = trees[0].Ndim(); // # of dimensions
Np = (unsigned long) mxGetScalar(prhs[1]); // # of points to sample
Niter = (unsigned int) mxGetScalar(prhs[2]); // # of gibbs iterations
if ((nrhs < 5) || (mxGetN(prhs[3]) == 0)) { // load analytic function
analyticFnParam = NULL; // params if required
}
else {
analyticFnParam = (mxArray**) mxMalloc(3*sizeof(mxArray*));
analyticFnParam[0] = (mxArray*) prhs[3];
analyticFnParam[1] = (mxArray*) prhs[4];
}
pointsM = plhs[0] = mxCreateDoubleMatrix(Ndim, Np, mxREAL); // set up matlab output
points = (double*) mxGetData(plhs[0]);
// plhs[1] = mxCreateDoubleMatrix(1, Np, mxREAL);
// weights = (double*) mxGetData(plhs[1]);
plhs[1] = mxCreateNumericMatrix(Ndens, Np, mxUINT32_CLASS, mxREAL);
indices = (BallTree::index*) mxGetData(plhs[1]);
unsigned long maxNp = Np; // largest # of particles we deal with
for (unsigned int j=0; j<Ndens; j++) // compute Max Np over all densities
if (maxNp < trees[j].Npts()) maxNp = trees[j].Npts();
unsigned int Nlevels = (unsigned int) (log((double)maxNp)/log((double)2))+1; // how many levels to a balanced binary tree?
// Generate enough random numbers to get us through the rest of this
aRandParam = mxCreateDoubleMatrix(1, 2, mxREAL);
pRandParam = mxGetPr(aRandParam);
pRandParam[0] = 1; pRandParam[1] = Np*Ndens*(Niter+1)*Nlevels;
mexCallMATLAB(1, &aRandVec, 1, &aRandParam, "rand"); randU = mxGetPr(aRandVec);
pRandParam[0] = 1; pRandParam[1] = Ndim*Np*(Niter+1)*Nlevels;
mexCallMATLAB(1, &aRandVecN, 1, &aRandParam, "randn"); randN = mxGetPr(aRandVecN);
mxDestroyArray(aRandParam);
// Params: Ndens, trees, points, weights, indices, randomU, randomN
gibbs2(Ndens,trees,Np,Niter,points,indices, randU,randN);
delete[] trees;
if (analyticFnParam != NULL)
mxFree(analyticFnParam);
mxDestroyArray(aRandVec);
mxDestroyArray(aRandVecN);
}
void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
int i,j, k, status,buflen,Cnt, Hndl, L,M,N, NumHandles, commandswitch;
int *HndlArray;
mxArray *mymxArray;
double *myDblPr;
chtype RequestType;
char PVName[PV_NAME_LENGTH_MAX+1];
// char MCAMessageString[MCA_MESSAGE_STRING_LENGTH_MAX+1];
dbr_string_t StrBuffer;
const char *MCAInfoFields[]={"PVName","ElementCount","NativeType","State","MCAMessage","Host"};
char *NativeTypeStrings[] = {"STRING","INT","FLOAT","ENUM","CHAR","LONG","DOUBLE"};
if(!CA_INITIALIZED) // Initialize CA if not initialized (first call)
{ mexPrintf("Initializing MATLAB Channel Access ... \n");
status = ca_task_initialize();
if(status!=ECA_NORMAL)
mexErrMsgTxt("Unable to initialise Challel Access\n");
CA_INITIALIZED = true;
// Register a function to be called when a this mex-file is cleared from memory
// with 'clear' or when exitting MATLAB
mexAtExit(mca_cleanup);
// Lock the mex-file so that it can not be cleared without explicitly
// mexUnclock
mexLock();
//start periodic polling:
/* PollTimerHandle = SetTimer(NULL,NULL,MCA_POLL_PERIOD,background_poll);
if(PollTimerHandle)
mexPrintf("Periodic CA polling started! System Timer ID: %u\n",PollTimerHandle);
else
mexWarnMsgTxt("Failed to start periodic CA polling\n");
*/
}
commandswitch = (int)mxGetScalar(prhs[0]);
switch(commandswitch)
{ case 0:
mexUnlock();
break;
case 1: // MCAOPEN - add channel(s) by PV names, all arguments following prhs[0]
// must be strings - names of PV's
for(i=1;i<nrhs;i++)
{ mxGetString(prhs[i],PVName,PV_NAME_LENGTH_MAX+1);
status = ca_search(PVName,&(CHNLS[HandlesUsed].CHID));
if(status == ECA_NORMAL) // if not - go on to the next PV name
{ status = ca_pend_io(MCA_SEARCH_TIMEOUT);
if (status == ECA_NORMAL)
{ // Allocate persistent memory for the DataBuffer on this channel
// to hold all elements of the DBR_XXX type
// nearest to the native type
// RequestType = dbf_type_to_DBR(ca_field_type(CHNLS[HandlesUsed].CHID));
// Cnt=ca_element_count(CHNLS[HandlesUsed].CHID);
CHNLS[HandlesUsed].NumElements = ca_element_count(CHNLS[HandlesUsed].CHID);
CHNLS[HandlesUsed].NativeType2DBR = dbf_type_to_DBR(ca_field_type(CHNLS[HandlesUsed].CHID));
CHNLS[HandlesUsed].MonitorEventCount = 0;
switch(CHNLS[HandlesUsed].NativeType2DBR)
{ case DBR_STRING:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_string_t));
break;
case DBR_INT: // As defined in db_access.h DBR_INT = DBR_SHORT = 1
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_short_t));
break;
case DBR_FLOAT:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_float_t));
break;
case DBR_ENUM:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_enum_t));
break;
case DBR_CHAR:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_char_t));
break;
case DBR_LONG:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_short_t));
break;
case DBR_DOUBLE:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_double_t));
break;
}
mexMakeMemoryPersistent(CHNLS[HandlesUsed].DataBuffer);
if(CHNLS[HandlesUsed].NativeType2DBR==DBR_STRING) // CACHE
{ if(CHNLS[HandlesUsed].NumElements==1) // Create MATLAB string - originally empty
CHNLS[HandlesUsed].CACHE = mxCreateString("");
else // Create MATLAB cell array of strings
{ CHNLS[HandlesUsed].CACHE = mxCreateCellMatrix(1,CHNLS[HandlesUsed].NumElements);
for(k=0;k<CHNLS[HandlesUsed].NumElements;k++)
{ mymxArray = mxCreateString("");
mexMakeArrayPersistent(mymxArray);
mxSetCell(CHNLS[HandlesUsed].CACHE, k, mymxArray);
}
}
}
else // Make CACHE a numeric mxArray
{ CHNLS[HandlesUsed].CACHE = mxCreateDoubleMatrix(1,CHNLS[HandlesUsed].NumElements,mxREAL);
}
mexMakeArrayPersistent(CHNLS[HandlesUsed].CACHE);
plhs[i-1]=mxCreateScalarDouble(++HandlesUsed);
}
else
plhs[i-1]=mxCreateScalarDouble(0);
}
else
plhs[i-1]=mxCreateScalarDouble(0);
} break;
case 2:// MCAOPEN - add channel(s) by PV names. The arguments following prhs[0]
// argument must be a cell array of strings - PV names
L = mxGetM(prhs[1])*mxGetN(prhs[1]);
plhs[0] = mxCreateDoubleMatrix(1,L,mxREAL);
myDblPr = mxGetPr(plhs[0]);
for(i=0;i<L;i++)
{ mymxArray = mxGetCell(prhs[1],i);
mxGetString(mymxArray,PVName,PV_NAME_LENGTH_MAX+1);
status = ca_search(PVName,&(CHNLS[HandlesUsed].CHID));
if(status == ECA_NORMAL) // if not - go on to the next PV name
{ status = ca_pend_io(MCA_IO_TIMEOUT);
if (status == ECA_NORMAL)
{ // Allcate persistent memory for the DataBuffer on this channel
//RequestType = dbf_type_to_DBR(ca_field_type(CHNLS[HandlesUsed].CHID));
CHNLS[HandlesUsed].NativeType2DBR = dbf_type_to_DBR(ca_field_type(CHNLS[HandlesUsed].CHID));
CHNLS[HandlesUsed].NumElements = ca_element_count(CHNLS[HandlesUsed].CHID);
CHNLS[HandlesUsed].MonitorEventCount = 0;
//Cnt=ca_element_count(CHNLS[HandlesUsed].CHID);
switch(CHNLS[HandlesUsed].NativeType2DBR)
{ case DBR_STRING:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_string_t));
break;
case DBR_INT: // As defined in db_access.h DBR_INT = DBR_SHORT = 1
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_short_t));
break;
case DBR_FLOAT:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_float_t));
break;
case DBR_ENUM:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_enum_t));
break;
case DBR_CHAR:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_char_t));
break;
case DBR_LONG:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_short_t));
break;
case DBR_DOUBLE:
CHNLS[HandlesUsed].DataBuffer = mxCalloc(CHNLS[HandlesUsed].NumElements,sizeof(dbr_double_t));
break;
}
mexMakeMemoryPersistent(CHNLS[HandlesUsed].DataBuffer);
if(CHNLS[HandlesUsed].NativeType2DBR == DBR_STRING) // CACHE
{ CHNLS[HandlesUsed].CACHE = mxCreateCellMatrix(1,CHNLS[HandlesUsed].NumElements);
for(k=0;k<CHNLS[HandlesUsed].NumElements;k++)
{ mymxArray = mxCreateString(StrBuffer);
mexMakeArrayPersistent(mymxArray);
mxSetCell(CHNLS[HandlesUsed].CACHE, k, mymxArray);
}
}
else
{ CHNLS[HandlesUsed].CACHE = mxCreateDoubleMatrix(1,CHNLS[HandlesUsed].NumElements,mxREAL);
}
mexMakeArrayPersistent(CHNLS[HandlesUsed].CACHE);
myDblPr[i] = ++HandlesUsed;
}
else
myDblPr[i] = 0;
}
else
myDblPr[i] = 0;
} break;
case 3: // MCAOPEN Return names of connected channels as cell array of strings
plhs[0] = mxCreateCellArray(1, &HandlesUsed);
for(i=0;i<HandlesUsed;i++)
{ if(CHNLS[i].CHID!=NULL)
{ mymxArray = mxCreateString(ca_name(CHNLS[i].CHID));
mxSetCell(plhs[0], i, mymxArray);
}
else
{ mymxArray = mxCreateString("");
//mexPrintf("Handle: %d PV: %s\n",i+1, "Cleared Channel");
mxSetCell(plhs[0], i, mymxArray);
}
} break;
case 5: // MCACLOSE permanently clear channel
Hndl = (int)mxGetScalar(prhs[1]);
if(Hndl<1 || Hndl>HandlesUsed)
mexErrMsgTxt("Handle out of range");
// If a monitor is installed, set the EVID pointer to NULL
// ca_clear_event dos not do it by itself
if(CHNLS[Hndl-1].EVID)
CHNLS[Hndl-1].EVID = NULL;
// If there is Callback String - destroy it
if(CHNLS[Hndl-1].MonitorCBString)
{ mxFree(CHNLS[Hndl-1].MonitorCBString);
CHNLS[Hndl-1].MonitorCBString =NULL;
}
if(ca_state(CHNLS[Hndl-1].CHID)==3)
mexWarnMsgTxt("Channel previously cleared");
else
if(ca_clear_channel(CHNLS[Hndl-1].CHID)!=ECA_NORMAL)
mexErrMsgTxt("ca_clear_channel failed");
break;
case 10: // MCAINFO return channels info as MATLAB structure array
if(HandlesUsed>0)
{ plhs[0] = mxCreateStructMatrix(1,HandlesUsed,6,MCAInfoFields);
for(i=0;i<HandlesUsed;i++)
{ mxSetFieldByNumber(plhs[0],i,0,mxCreateString(ca_name(CHNLS[i].CHID)));
mxSetFieldByNumber(plhs[0],i,1,mxCreateScalarDouble(ca_element_count(CHNLS[i].CHID)));
mxSetFieldByNumber(plhs[0],i,5,mxCreateString(ca_host_name(CHNLS[i].CHID)));
switch(ca_state(CHNLS[i].CHID))
{ case 1: // Disconnected due to Server or Network - may reconnect
mxSetFieldByNumber(plhs[0],i,2,mxCreateString("unknown"));
mxSetFieldByNumber(plhs[0],i,3,mxCreateString("disconnected"));
mxSetFieldByNumber(plhs[0],i,4,mxCreateString("Disconnected due to server or network problem"));
break;
case 2: // Normal connection
mxSetFieldByNumber(plhs[0],i,2,mxCreateString(NativeTypeStrings[ca_field_type(CHNLS[i].CHID)]));
mxSetFieldByNumber(plhs[0],i,3,mxCreateString("connected"));
mxSetFieldByNumber(plhs[0],i,4,mxCreateString("Normal connection"));
break;
case 3: // Disconnected by user
mxSetFieldByNumber(plhs[0],i,2,mxCreateString("unknown"));
mxSetFieldByNumber(plhs[0],i,3,mxCreateString("disconnected"));
mxSetFieldByNumber(plhs[0],i,4,mxCreateString("Permanently disconnected (cleared) by the user"));
break;
}
}
}
else
{ mexWarnMsgTxt("No connected PV's found");
plhs[0] = mxCreateDoubleMatrix(0,0,mxREAL);
}
break;
case 11: // MCAINFO return info for 1 channel by handle number
Hndl = (int)mxGetScalar(prhs[1]);
if(Hndl<1 || Hndl>HandlesUsed)
mexErrMsgTxt("Handle out of range");
plhs[0] = mxCreateStructMatrix(1,1,6,MCAInfoFields);
mxSetFieldByNumber(plhs[0],0,0,mxCreateString(ca_name(CHNLS[Hndl-1].CHID)));
mxSetFieldByNumber(plhs[0],0,1,mxCreateScalarDouble(ca_element_count(CHNLS[Hndl-1].CHID)));
mxSetFieldByNumber(plhs[0],0,5,mxCreateString(ca_host_name(CHNLS[Hndl-1].CHID)));
switch(ca_state(CHNLS[Hndl-1].CHID))
{ case 1: // Disconnected due to Server or Network - may reconnect
mxSetFieldByNumber(plhs[0],0,2,mxCreateString("unknown"));
mxSetFieldByNumber(plhs[0],0,3,mxCreateString("disconnected"));
mxSetFieldByNumber(plhs[0],0,4,mxCreateString("Disconnected due to server or network problem"));
break;
case 2: // Normal connection
mxSetFieldByNumber(plhs[0],0,2,mxCreateString(NativeTypeStrings[ca_field_type(CHNLS[Hndl-1].CHID)]));
mxSetFieldByNumber(plhs[0],0,3,mxCreateString("connected"));
mxSetFieldByNumber(plhs[0],0,4,mxCreateString("Normal connection"));
break;
case 3: // Disconnected by user
mxSetFieldByNumber(plhs[0],0,2,mxCreateString("unknown"));
mxSetFieldByNumber(plhs[0],0,3,mxCreateString("disconnected"));
mxSetFieldByNumber(plhs[0],0,4,mxCreateString("Permanently disconnected (cleared) by the user"));
break;
};
break;
case 12: // MCASTATE return an array of status (1 - OK, 0 - disconnected or cleared)
if(HandlesUsed>0)
{ plhs[0] = mxCreateDoubleMatrix(1,HandlesUsed,mxREAL);
myDblPr = mxGetPr(plhs[0]);
for(i=0;i<HandlesUsed;i++)
myDblPr[i] = (double)(ca_state(CHNLS[i].CHID)==2);
}
else
{ mexWarnMsgTxt("No connected PV's found");
plhs[0] = mxCreateDoubleMatrix(0,0,mxREAL);
}
break;
case 30: // poll
ca_poll();
break;
case 50: // MCAGET Get PV values by their MCA handles
for(i=0;i<nrhs-1;i++) // First loop: place all ca_get requests in the buffer
{ Hndl = (int)mxGetScalar(prhs[1+i]); //start from[1]: [0] argument is the commnads switch
if(Hndl<1 || Hndl>HandlesUsed)
mexErrMsgTxt("Invalid Handle");
RequestType = dbf_type_to_DBR(ca_field_type(CHNLS[Hndl-1].CHID));
Cnt = ca_element_count(CHNLS[Hndl-1].CHID);
status = ca_array_get(RequestType,Cnt,CHNLS[Hndl-1].CHID,CHNLS[Hndl-1].DataBuffer);
if(status!=ECA_NORMAL)
mexPrintf("Error in call to ca_array_get\n");
}
status = ca_pend_io(MCA_GET_TIMEOUT);
if(status!=ECA_NORMAL)
mexErrMsgTxt("... ca_pend_io call timed out \n");
for(i=0;i<nrhs-1;i++) // Another loop to copy data from temp structures to MATLAB
{ Hndl = (int)mxGetScalar(prhs[1+i]);
RequestType = RequestType = dbf_type_to_DBR(ca_field_type(CHNLS[Hndl-1].CHID));
Cnt = ca_element_count(CHNLS[Hndl-1].CHID);
if(RequestType==DBR_STRING)
{ if(Cnt==1)
plhs[i] = mxCreateString((char*)(*((dbr_string_t*)(CHNLS[Hndl-1].DataBuffer))));
else
{ plhs[i] = mxCreateCellMatrix(1,Cnt);
for(j=0;j<Cnt;j++)
mxSetCell(plhs[i], j, mxCreateString((char*)(*((dbr_string_t*)(CHNLS[Hndl-1].DataBuffer)+j))));
}
}
else
{ plhs[i] = mxCreateDoubleMatrix(1,Cnt,mxREAL);
myDblPr = mxGetPr(plhs[i]);
switch(dbf_type_to_DBR(ca_field_type(CHNLS[Hndl-1].CHID)))
{ case DBR_INT: // As defined in db_access.h DBR_INT = DBR_SHORT = 1
for(j=0;j<Cnt;j++)
myDblPr[j]= (double)(*((dbr_short_t*)(CHNLS[Hndl-1].DataBuffer)+j));
break;
case DBR_FLOAT:
for(j=0;j<Cnt;j++)
myDblPr[j]= (double)(*((dbr_float_t*)(CHNLS[Hndl-1].DataBuffer)+j));
break;
case DBR_ENUM:
for(j=0;j<Cnt;j++)
myDblPr[j]= (double)(*((dbr_enum_t*)(CHNLS[Hndl-1].DataBuffer)+j));
break;
case DBR_CHAR:
for(j=0;j<Cnt;j++)
myDblPr[j]= (double)(*((dbr_char_t*)(CHNLS[Hndl-1].DataBuffer)+j));
break;
case DBR_LONG:
for(j=0;j<Cnt;j++)
myDblPr[j]= (double)(*((dbr_long_t*)(CHNLS[Hndl-1].DataBuffer)+j));
break;
case DBR_DOUBLE:
for(j=0;j<Cnt;j++)
myDblPr[j]= (double)(*((dbr_double_t*)(CHNLS[Hndl-1].DataBuffer)+j));
break;
}
}
} break;
case 51: // MCAGET Get scalar PV of the same type
// second argument is an array of handles
// returns an array of values
myDblPr = mxGetPr(prhs[1]);
M = mxGetM(prhs[1]);
N = mxGetN(prhs[1]);
NumHandles = M*N;
plhs[0] = mxCreateDoubleMatrix(M,N,mxREAL);
for(i=0;i<NumHandles;i++) // First loop: place all ca_get requests in the buffer
{ Hndl = (int)myDblPr[i];
if(Hndl<1 || Hndl>HandlesUsed)
mexErrMsgTxt("Invalid Handle");
RequestType = dbf_type_to_DBR(ca_field_type(CHNLS[Hndl-1].CHID));
status = ca_array_get(DBR_DOUBLE,1,CHNLS[Hndl-1].CHID,mxGetPr(plhs[0])+i);
if(status!=ECA_NORMAL)
mexPrintf("Error in call to ca_array_get\n");
}
status = ca_pend_io(MCA_GET_TIMEOUT);
if(status!=ECA_NORMAL)
mexErrMsgTxt("... ca_pend_io call timed out \n");
break;
case 70: // MCAPUT
NumHandles = (nrhs-1)/2;
for(i=0;i<NumHandles;i++)
{ j = 2+i*2;
Hndl = (int)mxGetScalar(prhs[1+i*2]);
if(Hndl<1 || Hndl>HandlesUsed)
mexErrMsgTxt("Handle out of range - no values written");
// Set the status to 0 - mcaput_callback will write 1, if successful
CHNLS[Hndl-1].LastPutStatus = 0;
RequestType = dbf_type_to_DBR(ca_field_type(CHNLS[Hndl-1].CHID));
Cnt = ca_element_count(CHNLS[Hndl-1].CHID);
// If a value to write is passed as a string - the number of elements to write
// is 1 , NOT the length of the string returned by mxGetNumberOfElements
if(mxIsChar(prhs[j]))
L=1;
else
L = min(mxGetNumberOfElements(prhs[j]),Cnt);
// Copy double or string data from MATLAB prhs[] to DataBuffer
// on each channel
if(RequestType==DBR_STRING)
{ // STRING type is is passed as a cell array of strings
// A a 1-row MATLAB character array (1 string) may also be passed as a value
if(mxIsChar(prhs[j]))
{ mxGetString(prhs[j], StrBuffer, sizeof(dbr_string_t));
strcpy((char*)(*((dbr_string_t*)(CHNLS[Hndl-1].DataBuffer))),StrBuffer);
}
else if(mxIsCell(prhs[j]))
{ for(k=0;k<L;k++)
{ mxGetString(mxGetCell(prhs[j],k), StrBuffer, sizeof(dbr_string_t));
strcpy((char*)(*((dbr_string_t*)(CHNLS[Hndl-1].DataBuffer)+k)),StrBuffer);
}
}
}
else
{ myDblPr = mxGetPr(prhs[j]);
switch(RequestType)
{
case DBR_INT: // As defined in db_access.h DBR_INT = DBR_SHORT = 1
for(k=0;k<L;k++)
*((dbr_short_t*)(CHNLS[Hndl-1].DataBuffer)+k) = (dbr_short_t)(myDblPr[k]);
break;
case DBR_FLOAT:
for(k=0;k<L;k++)
*((dbr_float_t*)(CHNLS[Hndl-1].DataBuffer)+k) = (dbr_float_t)(myDblPr[k]);
break;
case DBR_ENUM:
for(k=0;k<L;k++)
*((dbr_enum_t*)(CHNLS[Hndl-1].DataBuffer)+k) = (dbr_enum_t)(myDblPr[k]);
break;
case DBR_CHAR:
for(k=0;k<L;k++)
*((dbr_char_t*)(CHNLS[Hndl-1].DataBuffer)+k) = (dbr_char_t)(myDblPr[k]);
break;
case DBR_LONG:
for(k=0;k<L;k++)
*((dbr_long_t*)(CHNLS[Hndl-1].DataBuffer)+k) = (dbr_long_t)(myDblPr[k]);
break;
case DBR_DOUBLE:
for(k=0;k<L;k++)
*((dbr_double_t*)(CHNLS[Hndl-1].DataBuffer)+k) = (dbr_double_t)(myDblPr[k]);
break;
}
}
// place request in the que
status = ca_array_put_callback(RequestType,L,CHNLS[Hndl-1].CHID,CHNLS[Hndl-1].DataBuffer,
mcaput_callback,&(CHNLS[Hndl-1].LastPutStatus));
if(status!=ECA_NORMAL)
mexPrintf("ca_array_put_callback failed\n");
}
status = ca_pend_event(MCA_PUT_TIMEOUT);
plhs[0]=mxCreateDoubleMatrix(1,NumHandles,mxREAL);
myDblPr = mxGetPr(plhs[0]);
for(i=0;i<NumHandles;i++)
{ Hndl = (int)mxGetScalar(prhs[1+i*2]);
myDblPr[i] = (double)CHNLS[Hndl-1].LastPutStatus;
}
break;
case 80: // MCAPUT - fast unconfirmed put for scalar numeric PV's
myDblPr = mxGetPr(prhs[1]);
M = mxGetM(prhs[1]);
N = mxGetN(prhs[1]);
NumHandles = M*N;
plhs[0] = mxCreateDoubleMatrix(M,N,mxREAL);
myDblPr = mxGetPr(plhs[0]);
for(i=0;i<NumHandles;i++)
{ myDblPr = mxGetPr(plhs[0]);
Hndl = (int)(*(mxGetPr(prhs[1])+i));
if(Hndl<1 || Hndl>HandlesUsed)
mexErrMsgTxt("Handle out of range - no values written");
status = ca_array_put(DBR_DOUBLE,1,CHNLS[Hndl-1].CHID,mxGetPr(prhs[2])+i);
if(status!=ECA_NORMAL)
{ myDblPr[i] = 0;
//mexPrintf("ca_array_put_callback failed\n");
}
else
{ myDblPr[i] = 1;
}
}
status = ca_pend_io(MCA_PUT_TIMEOUT);
break;
case 100: // MCAMON install Monitor or replace MonitorCBString
Hndl = (int)mxGetScalar(prhs[1]);
// Check if the handle is within range
if(Hndl<1 || Hndl>HandlesUsed)
{ plhs[0]=mxCreateScalarDouble(0);
mexErrMsgTxt("Invalid Handle");
}
if(CHNLS[Hndl-1].EVID) // if VID is not NULL - another monitor is already installed - replace MonitorCBString
{ if(CHNLS[Hndl-1].MonitorCBString) // Free memory for occupied by the old MonitorCBString
{ mxFree(CHNLS[Hndl-1].MonitorCBString);
CHNLS[Hndl-1].MonitorCBString = NULL;
}
if(nrhs>2) // Check if the new string is specified
{ if(mxIsChar(prhs[2]))
{ buflen = mxGetM(prhs[2])*mxGetN(prhs[2])+1;
CHNLS[Hndl-1].MonitorCBString = (char *)mxMalloc(buflen);
mexMakeMemoryPersistent(CHNLS[Hndl-1].MonitorCBString);
mxGetString(prhs[2],CHNLS[Hndl-1].MonitorCBString,buflen);
}
else
mexErrMsgTxt("Third argument must be a string\n");
}
plhs[0]=mxCreateScalarDouble(1);
}
else // No monitor is presently installed;
{ RequestType = dbf_type_to_DBR(ca_field_type(CHNLS[Hndl-1].CHID)); // Closest to the native
if(nrhs>2)
{ if(mxIsChar(prhs[2]))
{ buflen = mxGetM(prhs[2])*mxGetN(prhs[2])+1;
CHNLS[Hndl-1].MonitorCBString = (char *)mxMalloc(buflen);
mexMakeMemoryPersistent(CHNLS[Hndl-1].MonitorCBString);
mxGetString(prhs[2],CHNLS[Hndl-1].MonitorCBString,buflen);
}
else
mexErrMsgTxt("Third argument must be a string\n");
}
else
CHNLS[Hndl-1].MonitorCBString = NULL; // Set MonitorCBString to NULL so that mcaMonitorEventHandler only copies data to CACHE
// Count argument set to 0 - native count
status = ca_add_array_event(RequestType,0,CHNLS[Hndl-1].CHID, mcaMonitorEventHandler, &CHNLS[Hndl-1], 0.0, 0.0, 0.0, &(CHNLS[Hndl-1].EVID));
if(status!=ECA_NORMAL)
{ mexPrintf("ca_add_array_event failed\n");
plhs[0]=mxCreateScalarDouble(0);
}
else
{ ca_poll();
plhs[0]=mxCreateScalarDouble(1);
}
}
break;
case 200: // Clear Monitor MCACLEARMON
Hndl = (int)mxGetScalar(prhs[1]);
if(Hndl<1 || Hndl>HandlesUsed)
mexErrMsgTxt("Invalid Handle");
if(!CHNLS[Hndl-1].EVID)
mexErrMsgTxt("No monitor installed - can not clear");
status = ca_clear_event(CHNLS[Hndl-1].EVID);
if(status!=ECA_NORMAL)
mexPrintf("ca_clear_event failed\n");
// Set the EVID pointer to NULL (ca_clear_event dos not do it by itself)
// to use as a FLAG that no monitors are installed
CHNLS[Hndl-1].EVID = NULL;
// Reset
CHNLS[Hndl-1].MonitorEventCount = 0;
// If there is Callback String - destroy it
if(CHNLS[Hndl-1].MonitorCBString)
{ mxFree(CHNLS[Hndl-1].MonitorCBString);
CHNLS[Hndl-1].MonitorCBString =NULL;
}
break;
case 300: // MCACACHE Get Cached values of a monitored PV
for(i=0;i<nrhs-1;i++)
{ Hndl = (int)mxGetScalar(prhs[1+i]);
// if(Hndl<1 || Hndl>HandlesUsed || !CHNLS[Hndl-1].CACHE)
if(Hndl<1 || Hndl>HandlesUsed)
plhs[i] = mxCreateDoubleMatrix(0,0,mxREAL);
else
{ plhs[i] = mxDuplicateArray(CHNLS[Hndl-1].CACHE);
CHNLS[Hndl-1].MonitorEventCount = 0;
}
}
break;
case 500: // MCAMON Info on installed monitors
L = 0;
HndlArray = (int*)mxCalloc(HandlesUsed,sizeof(int));
for(i=0;i<HandlesUsed;i++) // Count installed monitors
{ if(CHNLS[i].EVID)
HndlArray[L++]=i+1;
}
if(L>0)
{ plhs[0] = mxCreateDoubleMatrix(1,L,mxREAL);
myDblPr = mxGetPr(plhs[0]);
plhs[1] = mxCreateCellMatrix(1,L);
for(i=0;i<L;i++)
{ myDblPr[i] = (double)HndlArray[i];
mxSetCell(plhs[1],i,mxCreateString(CHNLS[HndlArray[i]-1].MonitorCBString));
}
}
else
{ plhs[0] = mxCreateDoubleMatrix(0,0,mxREAL);
plhs[1] = mxCreateCellMatrix(0,0);
}
break;
case 510: // MCAMONEVENTS Event count fot monitors
plhs[0] = mxCreateDoubleMatrix(1,HandlesUsed,mxREAL);
myDblPr = mxGetPr(plhs[0]);
for(i=0;i<HandlesUsed;i++)
myDblPr[i]=(double)(CHNLS[i].MonitorEventCount);
break;
case 1000: // print timeout settings
plhs[0] = mxCreateDoubleMatrix(3,1,mxREAL);
mexPrintf("MCA timeout settings\n:");
mexPrintf("mcaopen\t%f [s]\n", MCA_SEARCH_TIMEOUT );
mexPrintf("mcaget\t%f [s]\n", MCA_GET_TIMEOUT );
mexPrintf("mcaput\t%f [s]\n", MCA_PUT_TIMEOUT );
myDblPr = mxGetPr(plhs[0]);
myDblPr[0] = MCA_SEARCH_TIMEOUT;
myDblPr[1] = MCA_GET_TIMEOUT;
myDblPr[2] = MCA_PUT_TIMEOUT;
break;
case 1001: // set MCA_SEARCH_TIMEOUT
// return delay value
MCA_SEARCH_TIMEOUT = mxGetScalar(prhs[1]);
plhs[0] = mxCreateScalarDouble(MCA_SEARCH_TIMEOUT);
break;
case 1002: // set MCA_GET_TIMEOUT
// return delay value
MCA_GET_TIMEOUT = mxGetScalar(prhs[1]);
plhs[0] = mxCreateScalarDouble(MCA_GET_TIMEOUT);
break;
case 1003: // set MCA_PUT_TIMEOUT
// return delay value
MCA_PUT_TIMEOUT = mxGetScalar(prhs[1]);
plhs[0] = mxCreateScalarDouble(MCA_PUT_TIMEOUT);
break;
}
}
bool mat_load_multi_array_vec2(MATFile *f, QString qsVarName, std::vector<std::vector<Array> > &vvA)
{
const char *name = 0;
bool bRes = false;
vvA.clear();
if (f != 0) {
mxArray *matlab_mat = matGetNextVariable(f, &name);
std::cout << name << std::endl;
bool bLoaded = false;
while (matlab_mat != 0 && !bLoaded) {
if (qsVarName == name) {
if (mxIsCell(matlab_mat)) {
mwSize cell_ndim = mxGetNumberOfDimensions(matlab_mat);
const mwSize *cell_dims = mxGetDimensions(matlab_mat);
//std::cout << "number of cell dimensions: " << cell_ndim << endl;
assert(cell_ndim == 2);
for (int dim_idx = 0; dim_idx < 2; ++dim_idx) {
std::cout << "extent of cell dim " << dim_idx << ": " << cell_dims[dim_idx] << std::endl;
}
uint N1 = cell_dims[0];
uint N2 = cell_dims[1];
//vvA.resize(N1, std::vector<Array>(N2, Array()));
for (uint i1 = 0; i1 < N1; ++i1) {
vvA.push_back(std::vector<Array>());
for (uint i2 = 0; i2 < N2; ++i2) {
/* get dimensions of the current cell */
mwIndex subs[2];
subs[0] = i1;
subs[1] = i2;
mwIndex cell_idx = mxCalcSingleSubscript(matlab_mat, cell_ndim, subs);
mxArray *E = mxGetCell(matlab_mat, cell_idx);
mwSize mat_ndim = mxGetNumberOfDimensions(E);
const mwSize *mat_dims = mxGetDimensions(E);
//std::cout << "number of cell element dimensions: " << mat_ndim << endl;
assert(mat_ndim == Array::dimensionality);
/* copy from matlab matrix to Array */
boost::array<typename Array::size_type, Array::dimensionality> array_shape;
for (uint i = 0; i < Array::dimensionality; ++i)
array_shape[i] = mat_dims[i];
Array B(array_shape, boost::fortran_storage_order());
uint nElements = B.num_elements();
if (nElements > 0) {
typename Array::element *data2 = B.data();
if (mxIsSingle(E)) {
float *pE = (float *)mxGetPr(E);
assert(pE != 0);
for (uint i = 0; i < nElements; ++i) {
*(data2 + i) = *pE;
++pE;
}
}
else {
double *pE = mxGetPr(E);
assert(pE != 0);
for (uint i = 0; i < nElements; ++i) {
*(data2 + i) = *pE;
++pE;
}
}
//vvA[i1][i2] = B;
/* copy to array with normal storage order */
// Array A = B; // this does not work!!! (storage order is of course copied at construction :)
Array A(array_shape);
A = B;
vvA.back().push_back(A);
}
}
}// cell elements
bRes = true;
}// is cell
else {
std::cout << "variable is not a cell array" << std::endl;
}
bLoaded = true;
}
mxDestroyArray(matlab_mat);
matlab_mat = 0;
if (!bLoaded)
matlab_mat = matGetNextVariable(f, &name);
}// variables
}
assert(bRes && "variable not found or could not open file");
return bRes;
}
// Takes a MATLAB variable and writes in in Mathematica form to link
void toMma(const mxArray *var, MLINK link) {
// the following may occur when retrieving empty struct fields
// it showsup as [] in MATLAB so we return {}
// note that non-existent variables are caught and handled in eng_get()
if (var == NULL) {
MLPutFunction(link, "List", 0);
return;
}
// get size information
mwSize depth = mxGetNumberOfDimensions(var);
const mwSize *mbDims = mxGetDimensions(var);
// handle zero-size arrays
if (mxIsEmpty(var)) {
if (mxIsChar(var))
MLPutString(link, "");
else
MLPutFunction(link, "List", 0);
return;
}
// translate dimension information to Mathematica order
std::vector<int> mmDimsVec(depth);
std::reverse_copy(mbDims, mbDims + depth, mmDimsVec.begin());
int *mmDims = &mmDimsVec[0];
int len = mxGetNumberOfElements(var);
// numerical (sparse or dense)
if (mxIsNumeric(var)) {
mxClassID classid = mxGetClassID(var);
// verify that var is of a supported class
switch (classid) {
case mxDOUBLE_CLASS:
case mxSINGLE_CLASS:
case mxINT32_CLASS:
case mxINT16_CLASS:
case mxUINT16_CLASS:
case mxINT8_CLASS:
case mxUINT8_CLASS:
break;
default:
putUnknown(var, link);
return;
}
if (mxIsSparse(var)) {
// Note: I realised that sparse arrays can only hold double precision numerical types
// in MATLAB R2013a. I will leave the below implementation for single precision & integer
// types in case future versions of MATLAB will add support for them.
int ncols = mxGetN(var); // number of columns
mwIndex *jc = mxGetJc(var);
mwIndex *ir = mxGetIr(var);
int nnz = jc[ncols]; // number of nonzeros
MLPutFunction(link, CONTEXT "matSparseArray", 4);
mlpPutIntegerList(link, jc, ncols + 1);
mlpPutIntegerList(link, ir, nnz);
// if complex, put as im*I + re
if (mxIsComplex(var)) {
MLPutFunction(link, "Plus", 2);
MLPutFunction(link, "Times", 2);
MLPutSymbol(link, "I");
switch (classid) {
case mxDOUBLE_CLASS:
MLPutReal64List(link, mxGetPi(var), nnz); break;
case mxSINGLE_CLASS:
MLPutReal32List(link, (float *) mxGetImagData(var), nnz); break;
case mxINT16_CLASS:
MLPutInteger16List(link, (short *) mxGetImagData(var), nnz); break;
case mxINT32_CLASS:
MLPutInteger32List(link, (int *) mxGetImagData(var), nnz); break;
default:
assert(false); // should never reach here
}
}
switch (classid) {
case mxDOUBLE_CLASS:
MLPutReal64List(link, mxGetPr(var), nnz); break;
case mxSINGLE_CLASS:
MLPutReal32List(link, (float *) mxGetData(var), nnz); break;
case mxINT16_CLASS:
MLPutInteger16List(link, (short *) mxGetData(var), nnz); break;
case mxINT32_CLASS:
MLPutInteger32List(link, (int *) mxGetData(var), nnz); break;
default:
assert(false); // should never reach here
}
MLPutInteger32List(link, mmDims, depth);
}
else // not sparse
{
MLPutFunction(link, CONTEXT "matArray", 2);
// if complex, put as im*I + re
if (mxIsComplex(var)) {
MLPutFunction(link, "Plus", 2);
MLPutFunction(link, "Times", 2);
MLPutSymbol(link, "I");
switch (classid) {
case mxDOUBLE_CLASS:
MLPutReal64Array(link, mxGetPi(var), mmDims, NULL, depth); break;
case mxSINGLE_CLASS:
MLPutReal32Array(link, (float *) mxGetImagData(var), mmDims, NULL, depth); break;
case mxINT32_CLASS:
MLPutInteger32Array(link, (int *) mxGetImagData(var), mmDims, NULL, depth); break;
case mxINT16_CLASS:
MLPutInteger16Array(link, (short *) mxGetImagData(var), mmDims, NULL, depth); break;
case mxUINT16_CLASS:
{
int *arr = new int[len];
unsigned short *mbData = (unsigned short *) mxGetImagData(var);
std::copy(mbData, mbData + len, arr);
MLPutInteger32Array(link, arr, mmDims, NULL, depth);
delete [] arr;
break;
}
case mxINT8_CLASS:
{
short *arr = new short[len];
char *mbData = (char *) mxGetImagData(var);
std::copy(mbData, mbData + len, arr);
MLPutInteger16Array(link, arr, mmDims, NULL, depth);
delete [] arr;
break;
}
case mxUINT8_CLASS:
{
short *arr = new short[len];
unsigned char *mbData = (unsigned char *) mxGetImagData(var);
std::copy(mbData, mbData + len, arr);
MLPutInteger16Array(link, arr, mmDims, NULL, depth);
delete [] arr;
break;
}
default:
assert(false); // should never reach here
}
}
switch (classid) {
case mxDOUBLE_CLASS:
MLPutReal64Array(link, mxGetPr(var), mmDims, NULL, depth); break;
case mxSINGLE_CLASS:
MLPutReal32Array(link, (float *) mxGetData(var), mmDims, NULL, depth); break;
case mxINT32_CLASS:
MLPutInteger32Array(link, (int *) mxGetData(var), mmDims, NULL, depth); break;
case mxINT16_CLASS:
MLPutInteger16Array(link, (short *) mxGetData(var), mmDims, NULL, depth); break;
case mxUINT16_CLASS:
{
int *arr = new int[len];
unsigned short *mbData = (unsigned short *) mxGetData(var);
std::copy(mbData, mbData + len, arr);
MLPutInteger32Array(link, arr, mmDims, NULL, depth);
delete [] arr;
break;
}
case mxINT8_CLASS:
{
short *arr = new short[len];
char *mbData = (char *) mxGetData(var);
std::copy(mbData, mbData + len, arr);
MLPutInteger16Array(link, arr, mmDims, NULL, depth);
delete [] arr;
break;
}
case mxUINT8_CLASS:
{
short *arr = new short[len];
unsigned char *mbData = (unsigned char *) mxGetData(var);
std::copy(mbData, mbData + len, arr);
MLPutInteger16Array(link, arr, mmDims, NULL, depth);
delete [] arr;
break;
}
default:
assert(false); // should never reach here
}
MLPutInteger32List(link, mmDims, depth);
}
}
// logical (sparse or dense)
else if (mxIsLogical(var))
if (mxIsSparse(var)) {
int ncols = mxGetN(var); // number of columns
mwIndex *jc = mxGetJc(var);
mwIndex *ir = mxGetIr(var);
mxLogical *logicals = mxGetLogicals(var);
int nnz = jc[ncols]; // number of nonzeros
MLPutFunction(link, CONTEXT "matSparseLogical", 4);
mlpPutIntegerList(link, jc, ncols + 1);
mlpPutIntegerList(link, ir, nnz);
short *integers = new short[nnz];
std::copy(logicals, logicals+nnz, integers);
MLPutInteger16List(link, integers, nnz);
MLPutInteger32List(link, mmDims, depth);
delete [] integers;
}
else // not sparse
{
mxLogical *logicals = mxGetLogicals(var);
short *integers = new short[len];
std::copy(logicals, logicals+len, integers);
MLPutFunction(link, CONTEXT "matLogical", 2);
MLPutInteger16Array(link, integers, mmDims, NULL, depth);
MLPutInteger32List(link, mmDims, depth);
delete [] integers;
}
// char array
else if (mxIsChar(var)) {
assert(sizeof(mxChar) == sizeof(unsigned short));
// 1 by N char arrays (row vectors) are sent as a string
if (depth == 2 && mbDims[0] == 1) {
const mxChar *str = mxGetChars(var);
MLPutFunction(link, CONTEXT "matString", 1);
MLPutUTF16String(link, reinterpret_cast<const unsigned short *>(str), len); // cast may be required on other platforms: (mxChar *) str
}
// general char arrays are sent as an array of characters
else {
MLPutFunction(link, CONTEXT "matCharArray", 2);
const mxChar *str = mxGetChars(var);
MLPutFunction(link, "List", len);
for (int i=0; i < len; ++i)
MLPutUTF16String(link, reinterpret_cast<const unsigned short *>(str + i), 1);
MLPutInteger32List(link, mmDims, depth);
}
}
// struct
else if (mxIsStruct(var)) {
int nfields = mxGetNumberOfFields(var);
MLPutFunction(link, CONTEXT "matStruct", 2);
MLPutFunction(link, "List", len);
for (int j=0; j < len; ++j) {
MLPutFunction(link, "List", nfields);
for (int i=0; i < nfields; ++i) {
const char *fieldname;
fieldname = mxGetFieldNameByNumber(var, i);
MLPutFunction(link, "Rule", 2);
MLPutString(link, fieldname);
toMma(mxGetFieldByNumber(var, j, i), link);
}
}
MLPutInteger32List(link, mmDims, depth);
}
// cell
else if (mxIsCell(var)) {
MLPutFunction(link, CONTEXT "matCell", 2);
MLPutFunction(link, "List", len);
for (int i=0; i < len; ++i)
toMma(mxGetCell(var, i), link);
MLPutInteger32List(link, mmDims, depth);
}
// unknown or failure; TODO distinguish between unknown and failure
else
{
putUnknown(var, link);
}
}
/* The matlab mex function */
void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[] ) {
/* Vertex list input */
double *V;
/* Neighbour list input */
const mxArray *Ne;
mxArray *PneigMatlab;
mwSize *PneigDims;
int PneigLenght=0;
/* Outputs */
double *ET_table; /* Edge tangents table */
double *EV_table; /* Edge velocity */
double *ETV_index; /* Edge tangents/velocity index for tables */
double Ea, Eb, Ec, s, h, x, Tb3D_length, Vv;
double Np[3], Ns[3], Tb[3], Pm[3], X3[3], Y3[3], Tb3D[3];
double *Pn, *Pnop, *Pneig;
/* Current vertex */
double P[3]={0,0,0};
/* Table Size */
mwSize table_Dims[2]={1,3};
/* Number of vertices */
const mwSize *VertexDims;
int VertexN=0;
/* Number of indices */
int ETV_num=0;
/* Neighbour indices */
double neg;
int neg1, neg2;
/* Loop variables */
int i, j, k;
/* Check for proper number of arguments. */
if(nrhs!=2) {
mexErrMsgTxt("2 inputs are required.");
} else if(nlhs!=3) {
mexErrMsgTxt("3 output is required");
}
/* Connect Inputs */
V=(double *)mxGetPr(prhs[0]);
Ne=prhs[1];
/* Get number of VertexN */
VertexDims = mxGetDimensions(prhs[0]);
VertexN=VertexDims[0];
/* Reserve memory */
table_Dims[0]=VertexN*6; table_Dims[1]=3;
plhs[0]= mxCreateNumericArray(2, table_Dims, mxDOUBLE_CLASS, mxREAL);
table_Dims[0]=VertexN*6; table_Dims[1]=1;
plhs[1]= mxCreateNumericArray(2, table_Dims, mxDOUBLE_CLASS, mxREAL);
table_Dims[0]=VertexN*6; table_Dims[1]=2;
plhs[2] = mxCreateNumericArray(2, table_Dims, mxDOUBLE_CLASS, mxREAL);
/* Connect Outputs */
ET_table=(double *)mxGetPr(plhs[0]);
EV_table=(double *)mxGetPr(plhs[1]);
ETV_index=(double *)mxGetPr(plhs[2]);
Pn= (double *)malloc(VertexN*3*sizeof(double));
Pnop=(double *) malloc(VertexN*3*sizeof(double));
for (i=0; i<VertexN; i++) {
P[0]=V[i]; P[1]=V[i+VertexN]; P[2]=V[i+VertexN*2];
PneigMatlab=mxGetCell(Ne, i);
if( PneigMatlab == NULL)
{
PneigLenght=-1;
}
else
{
PneigDims=(mwSize *)mxGetDimensions(PneigMatlab);
PneigLenght=(PneigDims[0]*PneigDims[1]);
Pneig=(double *)mxGetPr(PneigMatlab);
}
/* Find the opposite vertex of each neigbourh vertex. */
/* incase of odd number of neigbourhs interpolate the opposite neigbourh */
if((PneigLenght%2)==0) {
for (k=0; k<PneigLenght; k++) {
neg =k+((double)PneigLenght)/2;
neg1=(int)floor(neg);
if(neg1>(PneigLenght-1)) { neg1=neg1-PneigLenght; }
Pn[k] =V[(int)Pneig[k]-1];
Pn[k+VertexN] =V[(int)Pneig[k]-1+VertexN];
Pn[k+VertexN*2]=V[(int)Pneig[k]-1+VertexN*2];
Pnop[k] =V[(int)Pneig[neg1]-1];
Pnop[k+VertexN] =V[(int)Pneig[neg1]-1+VertexN];
Pnop[k+VertexN*2]=V[(int)Pneig[neg1]-1+VertexN*2];
}
}
else {
for (k=0; k<PneigLenght; k++) {
neg=(double)k+((double)PneigLenght)*0.5;
neg1=(int)floor(neg); neg2=(int)ceil(neg);
if(neg1>(PneigLenght-1)) { neg1=neg1-PneigLenght; }
if(neg2>(PneigLenght-1)) { neg2=neg2-PneigLenght; }
Pn[k] =V[(int)Pneig[k]-1];
Pn[k+VertexN] =V[(int)Pneig[k]-1+VertexN];
Pn[k+VertexN*2]=V[(int)Pneig[k]-1+VertexN*2];
Pnop[k] =(V[(int)Pneig[neg1]-1] + V[(int)Pneig[neg2]-1])/2;
Pnop[k+VertexN] =(V[(int)Pneig[neg1]-1+VertexN] + V[(int)Pneig[neg2]-1+VertexN])/2;
Pnop[k+VertexN*2]=(V[(int)Pneig[neg1]-1+VertexN*2] + V[(int)Pneig[neg2]-1+VertexN*2])/2;
}
}
for(j=0;j<PneigLenght; j++) {
/* Calculate length edges of face */
Ec= sqrt(pow2(Pn[j]-P[0]) +pow2(Pn[j+VertexN]-P[1]) +pow2(Pn[j+VertexN*2]-P[2]))+1e-14;
Eb= sqrt(pow2(Pnop[j]-P[0]) +pow2(Pnop[j+VertexN]-P[1]) +pow2(Pnop[j+VertexN*2]-P[2]))+1e-14;
Ea= sqrt(pow2(Pn[j]-Pnop[j])+pow2(Pn[j+VertexN]-Pnop[j+VertexN]) +pow2(Pn[j+VertexN*2]-Pnop[j+VertexN*2]))+1e-14;
/* Calculate face surface area */
s = ((Ea+Eb+Ec)/2);
h = (2/Ea)*sqrt(s*(s-Ea)*(s-Eb)*(s-Ec))+1e-14;
x = (pow2(Ea)-pow2(Eb)+pow2(Ec))/(2*Ea);
/* Calculate tangent of 2D triangle */
Np[0]=-h / sqrt(pow2(-h)+pow2(x)); Np[1]= x / sqrt(pow2(-h)+pow2(x));
Ns[0]=h / sqrt(pow2(h)+pow2(Ea-x)); Ns[1]=(Ea-x) / sqrt(pow2(h)+pow2(Ea-x));
Tb[0]= Np[1]+Ns[1] ; Tb[1]=-(Np[0]+Ns[0]);
/* Back to 3D coordinates */
Pm[0]=(Pn[j]*x+Pnop[j]*(Ea-x))/Ea;
Pm[1]=(Pn[j+VertexN]*x+Pnop[j+VertexN]*(Ea-x))/Ea;
Pm[2]=(Pn[j+VertexN*2]*x+Pnop[j+VertexN*2]*(Ea-x))/Ea;
X3[0]=(Pn[j]-Pnop[j])/Ea;
X3[1]=(Pn[j+VertexN]-Pnop[j+VertexN])/Ea;
X3[2]=(Pn[j+VertexN*2]-Pnop[j+VertexN*2])/Ea;
Y3[0]=(P[0]-Pm[0])/h;
Y3[1]=(P[1]-Pm[1])/h;
Y3[2]=(P[2]-Pm[2])/h;
/* 2D tangent to 3D tangent */
Tb3D[0]=(X3[0]*Tb[0]+Y3[0]*Tb[1]);
Tb3D[1]=(X3[1]*Tb[0]+Y3[1]*Tb[1]);
Tb3D[2]=(X3[2]*Tb[0]+Y3[2]*Tb[1]);
Tb3D_length=sqrt(pow2(Tb3D[0])+pow2(Tb3D[1])+pow2(Tb3D[2]))+1e-14;
Tb3D[0]=Tb3D[0]/Tb3D_length;
Tb3D[1]=Tb3D[1]/Tb3D_length;
Tb3D[2]=Tb3D[2]/Tb3D_length;
/* Edge Velocity */
Vv=0.5*(Ec+0.5*Ea);
/* Store the data */
ETV_index[ETV_num]=i+1;
ETV_index[ETV_num+table_Dims[0]]=Pneig[j];
ET_table[ETV_num]=Tb3D[0];
ET_table[ETV_num+table_Dims[0]]=Tb3D[1];
ET_table[ETV_num+2*table_Dims[0]]=Tb3D[2];
EV_table[ETV_num]=Vv;
ETV_num++;
}
}
/* Remove temporary memory */
free(Pn);
free(Pnop);
}
void LTFAT_NAME(ltfatMexFnc)( int UNUSED(nlhs), mxArray *plhs[],
int UNUSED(nrhs), const mxArray *prhs[] )
{
static int atExitFncRegistered = 0;
if(!atExitFncRegistered)
{
LTFAT_NAME(ltfatMexAtExit)(LTFAT_NAME(fftblMexAtExitFnc));
atExitFncRegistered = 1;
}
const mxArray* mxF = prhs[0];
const mxArray* mxG = prhs[1];
double* foffDouble = (double*) mxGetData(prhs[2]);
double* a = (double*) mxGetData(prhs[3]);
double* realonlyDouble = (double*) mxGetData(prhs[4]);
// input data length
mwSize L = mxGetM(mxF);
// number of channels
mwSize W = mxGetN(mxF);
// filter number
mwSize M = mxGetNumberOfElements(mxG);
//
mwSize acols = mxGetN(prhs[3]);
double afrac[M];
memcpy(afrac,a,M*sizeof*a);
if(acols>1)
{
for(mwIndex m=0; m<M; m++)
{
afrac[m] = afrac[m]/a[M+m];
}
}
// output lengths
mwSize outLen[M];
// Frequency offsets
mwSignedIndex foff[M];
// realonly
int realonly[M];
// POINTER TO THE INPUT
LTFAT_COMPLEX* FPtr = mxGetData(prhs[0]);
// POINTER TO THE FILTERS
const LTFAT_COMPLEX* GPtrs[M];
// filter lengths
mwSize Gl[M];
// POINTER TO OUTPUTS
LTFAT_COMPLEX* cPtrs[M]; // C99 feature
plhs[0] = mxCreateCellMatrix(M, 1);
if(M!=LTFAT_NAME(oldM) || W != LTFAT_NAME(oldW))
{
LTFAT_NAME(fftblMexAtExitFnc)();
LTFAT_NAME(oldM) = M;
LTFAT_NAME(oldW) = W;
LTFAT_NAME(oldLc) = ltfat_calloc(M,sizeof(mwSize));
LTFAT_NAME(oldPlans) = ltfat_calloc(M,sizeof*LTFAT_NAME(oldPlans));
}
for(mwIndex m=0; m<M; ++m)
{
foff[m] = (mwSignedIndex) foffDouble[m];
realonly[m] = (realonlyDouble[m]>1e-3);
outLen[m] = (mwSize) floor( L/afrac[m] +0.5);
GPtrs[m] = mxGetData(mxGetCell(mxG, m));
Gl[m] = mxGetNumberOfElements(mxGetCell(mxG, m));
mxSetCell(plhs[0], m, ltfatCreateMatrix(outLen[m], W,
LTFAT_MX_CLASSID,mxCOMPLEX));
cPtrs[m] = mxGetData(mxGetCell(plhs[0],m));
if(LTFAT_NAME(oldLc)[m]!=outLen[m])
{
LTFAT_NAME(oldLc)[m] = outLen[m];
LTFAT_NAME(convsub_fftbl_plan) ptmp =
LTFAT_NAME(convsub_fftbl_init)( L, Gl[m], W, afrac[m], cPtrs[m]);
if(LTFAT_NAME(oldPlans)[m]!=0)
{
LTFAT_NAME(convsub_fftbl_done)(LTFAT_NAME(oldPlans)[m]);
}
LTFAT_NAME(oldPlans)[m]=ptmp;
}
}
LTFAT_NAME(filterbank_fftbl_execute)( LTFAT_NAME(oldPlans),FPtr, GPtrs, M,
foff, realonly, cPtrs);
}
void mexFunction( int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[] )
{
mxArray *rhs[2];
mxArray *blk_cell_pr, *A_cell_pr;
double *A, *B, *blksize;
mwIndex *irA, *jcA, *irB, *jcB;
mwIndex *cumblksize, *blknnz;
mwSize iscellA, mblk, mA, nA, m1, n1, rowidx, colidx, isspA, isspB;
mwIndex subs[2];
mwSize nsubs=2;
mwSize n, n2, k, nsub, index, numblk, NZmax;
double ir2=1/sqrt(2);
/* CHECK FOR PROPER NUMBER OF ARGUMENTS */
if (nrhs < 2){
mexErrMsgTxt("mexsmat: requires at least 2 input arguments."); }
else if (nlhs>1){
mexErrMsgTxt("mexsmat: requires 1 output argument."); }
/* CHECK THE DIMENSIONS */
iscellA = mxIsCell(prhs[1]);
if (iscellA) { mA = mxGetM(prhs[1]); nA = mxGetN(prhs[1]); }
else { mA = 1; nA = 1; }
if (mxGetM(prhs[0]) != mA) {
mexErrMsgTxt("mexsmat: blk and Avec not compatible"); }
/***** main body *****/
if (nrhs > 3) {rowidx = (mwSize)*mxGetPr(prhs[3]); } else {rowidx = 1;}
if (rowidx > mA) {
mexErrMsgTxt("mexsmat: rowidx exceeds size(Avec,1)."); }
subs[0] = rowidx-1; /* subtract 1 to adjust for Matlab index */
subs[1] = 1;
index = mxCalcSingleSubscript(prhs[0],nsubs,subs);
blk_cell_pr = mxGetCell(prhs[0],index);
if (blk_cell_pr == NULL) {
mexErrMsgTxt("mexsmat: blk not properly specified"); }
numblk = mxGetN(blk_cell_pr);
blksize = mxGetPr(blk_cell_pr);
cumblksize = mxCalloc(numblk+1,sizeof(mwSize));
blknnz = mxCalloc(numblk+1,sizeof(mwSize));
cumblksize[0] = 0; blknnz[0] = 0;
n = 0; n2 = 0;
for (k=0; k<numblk; ++k) {
nsub = (mwSize) blksize[k];
n += nsub;
n2 += nsub*(nsub+1)/2;
cumblksize[k+1] = n;
blknnz[k+1] = n2;
}
/***** assign pomwSizeers *****/
if (iscellA) {
subs[0] = rowidx-1;
subs[1] = 0;
index = mxCalcSingleSubscript(prhs[1],nsubs,subs);
A_cell_pr = mxGetCell(prhs[1],index);
A = mxGetPr(A_cell_pr);
m1 = mxGetM(A_cell_pr);
n1 = mxGetN(A_cell_pr);
isspA = mxIsSparse(A_cell_pr);
if (isspA) { irA = mxGetIr(A_cell_pr);
jcA = mxGetJc(A_cell_pr); }
} else {
A = mxGetPr(prhs[1]);
m1 = mxGetM(prhs[1]);
n1 = mxGetN(prhs[1]);
isspA = mxIsSparse(prhs[1]);
if (isspA) { irA = mxGetIr(prhs[1]);
jcA = mxGetJc(prhs[1]); }
}
if (numblk > 1)
{ isspB = 1; }
else {
if (nrhs > 2) {isspB = (mwSize)*mxGetPr(prhs[2]);} else {isspB = isspA;}
}
if (nrhs > 4) {colidx = (mwSize)*mxGetPr(prhs[4]) -1;} else {colidx = 0;}
if (colidx > n1) {
mexErrMsgTxt("mexsmat: colidx exceeds size(Avec,2).");
}
/***** create return argument *****/
if (isspB) {
if (isspA) { NZmax = jcA[colidx+1]-jcA[colidx]; }
else { NZmax = blknnz[numblk]; }
rhs[0] = mxCreateSparse(n,n,2*NZmax,mxREAL);
B = mxGetPr(rhs[0]); irB = mxGetIr(rhs[0]); jcB = mxGetJc(rhs[0]);
} else {
plhs[0] = mxCreateDoubleMatrix(n,n,mxREAL);
B = mxGetPr(plhs[0]);
}
/***** Do the computations in a subroutine *****/
if (numblk == 1) {
smat1(n,ir2,A,irA,jcA,isspA,m1,colidx,B,irB,jcB,isspB); }
else {
smat2(n,numblk,cumblksize,blknnz,ir2,A,irA,jcA,isspA,m1,colidx,B,irB,jcB,isspB);
}
if (isspB) {
/*** if isspB, (actual B) = B+B' ****/
mexCallMATLAB(1, &rhs[1], 1, &rhs[0], "transpose");
mexCallMATLAB(1, &plhs[0],2, rhs, "+");
mxDestroyArray(*rhs);
}
mxFree(blknnz);
mxFree(cumblksize);
return;
}
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
/* description:
* given a set of reference stimuli and responses (forming a joint distribution),
* this function will compute the log kernel density estimate over a grid of stimuli
* for a set of test responses. Within kernel types a radial-symmetric kernel is used. Different kernels are combined multiplicatively.
*
* syntax:
* out = kde_decode_general( stimulus, stimulus_grid, stimulus_kernel, stimulus_bandwidth, response, response_kernel, response_bandwidth, test_response[, offset[, distance[, timestamp, bins]]] );
*
* arguments:
* stimulus = number of spikes x number of stimulus dimensions
* stimulus_grid = number of grid elements x number of stimulus dimensions
* stimulus_kernel = 1 x number of stimulus dimensions
* stimulus_bandwidth = 1 x number of stimulus dimensions
* response = number of spikes x number of response dimensions
* response_kernel = 1 x number of response_dimensions
* response_bandwidth = 1 x number of response dimensions
* test_response = number of test spikes x number of response dimensions
* offset = number of grid elements
* distance = optional matrix of distances. If this argument is present (and not empty), the stimulus and stimulus_grid arguments should be given as a zero-based index into the distance matrix.
* timestamp = number of test spikes x 1
* bins = number of bins x 2
*
* out = number of test spikes x number of stimulus grid elements (if no timestamps and bins arguments are provided)
* out = number of bins x number of stimulus grid elements (if timestamps and bins arguments are provided)
*
* kernels:
* 0 = gaussian
* 1 = epanechnikov
* 2 = von mises
* 3 = kronecker
*
*/
double cutoff = 2; /* cut-off (in standard deviations) for gaussian kernel */
double vm_cutoff = 0.1; /* cut-off (probability) for von mises kernel */
static const double pi = 3.141592653589793238462643383279502884197;
/* INPUTS */
double *stimulus; /* NxQ */
double *stimulus_grid; /* GxQ */
double *stimulus_kernel; /* 1xQ */
double *stimulus_bandwidth; /* 1xQ */
double *response; /* NxD or Nx0 or empty*/
double *response_kernel; /* 1xD */
double *response_bandwidth; /* 1xD */
double *test_response; /* MxD or Mx0 or empty*/
double *timestamp;
double *bins;
double *stimulus_vonmises;
double *response_vonmises;
double *offset;
/* VARIABLES */
int N, D, M, Q, G, B;
int n, d, m, q, g, b;
int sizeM, loopM;
int next_idx, idx;
double *skip_g, *z;
double acc_a_gauss, acc_a_epa, acc_a_delta, acc_a_vm;
double *acc_g_gauss, *acc_g_epa, *acc_g_delta, *acc_g_vm;
double tmp;
double *pout, *pout2;
mxArray *out, *out2;
int idx1, idx2;
mxArray *tmpmat;
int *use_distance_lookup;
int *NI;
double **distance;
int ngauss = 0;
int nepa = 0;
int nmises = 0;
int nkron = 0;
double scaling_factor = 1;
double v;
double c1, c2;
mxArray *argout=NULL, *argin[2];
double *pargin1;
double *pargin2;
/* CHECK NUMBER OF INPUTS */
if (nrhs<4)
mexErrMsgTxt("This function requires at least four input arguments");
/* CHECK DIMENSIONS OF FIRST TWO ARGUMENTS */
if ( mxGetNumberOfDimensions(prhs[0])!=2 || mxGetNumberOfDimensions(prhs[1])!=2)
mexErrMsgTxt("stimulus and stimulus_grid input arguments need to be matrices");
/* GET POINTERS TO FIRST FOUR ARGUMENTS */
stimulus = mxGetPr( prhs[0] );
stimulus_grid = mxGetPr( prhs[1] );
stimulus_kernel = mxGetPr( prhs[2] );
stimulus_bandwidth = mxGetPr( prhs[3] );
/* GET ARRAY SIZES */
N = mxGetM( prhs[0] ); /* number of source (encoding) spikes */
Q = mxGetN( prhs[0] ); /* number of stimulus dimensions */
G = mxGetM( prhs[1] ); /* number of points in stimulus grid */
/* CHECK NUMBER OF DIMENSIONS IN STIMULUS GRID */
if (mxGetN(prhs[1])!=Q)
mexErrMsgTxt("Incompatible size of stimulus_grid input arguments");
/* CHECK NUMBER OF STIMULUS KERNELS AND BANDWIDTHS */
if (mxGetNumberOfElements(prhs[2])!=Q || mxGetNumberOfElements(prhs[3])!=Q)
mexErrMsgTxt("Incompatible size of stimulus kernel and/or bandwidth arguments");
/* CHECK OPTIONAL INPUTS */
/* CHECK IF EITHER NO RESPONSE, OR RESPONSE + KERNEL + BANDWIDTH IS SPECIFIED */
if (nrhs>5 && nrhs<7)
mexErrMsgTxt("Specify response, response kernel and bandwidth arguments");
if (nrhs>6) {
/* CHECK DIMENSIONALITY OF SPIKE RESPONSE (ENCODING)*/
if ( mxGetNumberOfDimensions(prhs[4])!=2 )
mexErrMsgTxt("Response input argument needs to be a matrix");
response = mxGetPr( prhs[4] );
D = mxGetN( prhs[4] ); /* number of response dimensions */
/* CHECK NUMBER OF SPIKES IN RESPONSE */
if ( (D>0 && mxGetM(prhs[4])!=N ) )
mexErrMsgTxt("Incompatible size of response input argument");
response_kernel = mxGetPr( prhs[5] );
response_bandwidth = mxGetPr( prhs[6] );
/* CHECK NUMBER OF RESPONSE KERNELS AND BANDWIDTHS */
if (mxGetNumberOfElements(prhs[5])!=D || mxGetNumberOfElements(prhs[6])!=D)
mexErrMsgTxt("Incompatible size of response kernel and/or bandwidth arguments");
} else {
D = 0; /* no response specified */
}
if (nrhs>7) {
/* CHECK DIMENSIONALITY OF TEST RESPONSE (DECODING)*/
if ( mxGetNumberOfDimensions(prhs[7])!=2 )
mexErrMsgTxt("Test_response input argument needs to be a matrix");
test_response = mxGetPr( prhs[7] );
M = mxGetM( prhs[7] ); /* number of test (decoding) spikes */
/* CHECK NUMBER OF DIMENSIONS IN TEST RESPONSE */
if ( mxGetN(prhs[7])!=D )
mexErrMsgTxt("Incompatible size of test_response input argument");
} else {
M = 0; /* no test spikes specified */
}
if ( D==0 && M==0 )
M = 1;
if (nrhs>8) {
/* CHECK SIZE OF OFFSET VECTOR */
if ( !mxIsDouble( prhs[8] ) || mxGetNumberOfElements( prhs[8] )!=G )
mexErrMsgTxt("Incompatible size of offset vector");
offset = mxGetPr( prhs[8] );
} else {
mexErrMsgTxt("Please provide offset vector");
}
/* ALLOCATE ARRAYS FOR DISTANCE LOOK-UP TABLES */
use_distance_lookup = (int*) mxCalloc( Q, sizeof(int) );
distance = (double**) mxCalloc( Q, sizeof(double*) );
NI = (int*) mxCalloc( Q, sizeof(int) ); /* size of distance LUTs */
/* INITIALIZE ARRAY */
for (q=0;q<Q;q++)
use_distance_lookup[q] = 0;
if (nrhs>9) {
/* CHECK CLASS AND SIZE OF DISTANCE LUTs */
if ( !mxIsCell( prhs[9] ) || mxGetNumberOfElements( prhs[9] )!=Q )
mexErrMsgTxt("Distance input argument needs to be a cell array with as many cells as stimulus dimensions");
for ( q=0 ; q<Q ; q++ ) {
tmpmat = mxGetCell( prhs[9], q );
if (tmpmat==NULL || mxIsEmpty(tmpmat)) {
use_distance_lookup[q] = 0;
} else {
/* CHECK SIZE OF DISTANCE LUT */
if ( mxGetNumberOfDimensions(tmpmat)!=2 || mxGetM( tmpmat )!=mxGetN( tmpmat ) )
mexErrMsgTxt("Distance arrays need to be square matrices");
distance[q] = (double*) mxGetPr( tmpmat );
NI[q] = mxGetM( tmpmat );
use_distance_lookup[q] = true;
/* when using distance LUT, the corresponding stimulus and stimulus grid should be indices into the LUT */
/* CHECK IF STIMULUS AND STIMULUS_GRID >=0 && <NI[q] */
for ( n=0; n<N; n++ ) {
if ( stimulus[n+q*N]<0 || stimulus[n+q*N]>=NI[q] )
mexErrMsgTxt("Invalid index");
}
for ( g=0; g<G; g++ ) {
if ( stimulus_grid[g+q*G]<0 || stimulus_grid[g+q*G]>=NI[q] )
mexErrMsgTxt("Invalid index");
}
}
}
}
B = 0; /* number of time bins */
if (nrhs>10) {
/* CHECK DIMENSIONALITY OF TEST (DECODING) SPIKE TIMESTAMPS */
if ( mxGetNumberOfDimensions(prhs[10])!=2 )
mexErrMsgTxt("Timestamp input argument needs to be a matrix");
timestamp = mxGetPr( prhs[10] );
/* CHECK SIZE OF TEST (DECODING) SPIKE TIMESTAMPS */
if ( mxGetM( prhs[10] )!=M || mxGetN( prhs[10] )!=1 )
mexErrMsgTxt("Incompatible size of timestamp input argument");
}
if (nrhs>11) {
/* CHECK DIMENSIONALITY AND SIZE OF TIME BINS ARGUMENT */
if ( mxGetNumberOfDimensions(prhs[11])!=2 || mxGetN(prhs[11])!=2)
mexErrMsgTxt("Bins input argument needs to be a Bx2 matrix");
B = mxGetM( prhs[11] ); /* number of time bins */
bins = mxGetPr( prhs[11] );
}
cutoff *= cutoff; /* transform gaussian kernel cut-off to variance*/
/* COMPUTE CUT-OFFS FOR VON MISES KERNELS */
/* AND COUNT NUMBER OF DIMENSIONS WITH GAUSSIAN/EPANECHNIKOV/KRONECKER/VONMISES KERNELS */
stimulus_vonmises = (double*) mxCalloc( Q, sizeof(double) );
response_vonmises = (double*) mxCalloc( D, sizeof(double) );
argin[0] = mxCreateDoubleScalar(0);
argin[1] = mxCreateDoubleScalar(0);
pargin1 = mxGetPr(argin[0]);
pargin2 = mxGetPr(argin[1]);
for (q=0; q<Q; q++) {
if (stimulus_kernel[q]==0) {
ngauss++;
} else if (stimulus_kernel[q]==1) {
nepa++;
} else if (stimulus_kernel[q]==2) {
nmises++;
pargin2[0] = stimulus_bandwidth[q];
mexCallMATLAB(1, &argout, 2, argin, "besseli");
stimulus_vonmises[q] = acos( log( vm_cutoff * 2*pi * mxGetScalar(argout) ) / stimulus_bandwidth[q] );
scaling_factor /= mxGetScalar(argout);
} else {
nkron++;
}
}
for (d=0; d<D; d++) {
if (response_kernel[d]==0) {
ngauss++;
} else if (response_kernel[d]==1) {
nepa++;
} else if (response_kernel[d]==2) {
nmises++;
pargin2[0] = response_bandwidth[d];
mexCallMATLAB(1, &argout, 2, argin, "besseli");
response_vonmises[d] = acos( log( vm_cutoff * 2*pi * mxGetScalar(argout) ) / response_bandwidth[d] );
scaling_factor /= mxGetScalar(argout);
} else {
nkron++;
}
}
/* COMPUTE SCALING FACTOR */
if (ngauss>0)
scaling_factor *= pow(2*pi,-((double)ngauss)/2);
if (nepa>0) {
/* compute volume of hypersphere */
pargin1[0] = ((double)nepa)/2 + 1;
mexCallMATLAB(1, &argout, 1, argin, "gamma" );
v = pow(pi,0.5*(double)(nepa))/mxGetScalar(argout);
scaling_factor *= 0.5*(double)(nepa+2)/v;
}
if (nmises>0) {
scaling_factor /= pow(2*pi,(double)nmises);
}
if (nkron>0) {
/* compute volume of hypersphere */
pargin1[0] = ((double)nkron)/2 + 1;
mexCallMATLAB(1, &argout, 1, argin, "gamma" );
v = pow(pi,((double)nkron)/2)/mxGetScalar(argout);
scaling_factor /= v;
}
/* ALLOCATE TEMPORARY ARRAYS AND OUTPUT ARRAYS */
acc_g_gauss = (double*) mxCalloc( G, sizeof(double) );
acc_g_epa = (double*) mxCalloc( G, sizeof(double) );
acc_g_delta = (double*) mxCalloc( G, sizeof(double) );
acc_g_vm = (double*) mxCalloc( G, sizeof(double) );
skip_g = (double*) mxCalloc( G, sizeof(double) );
if (B==0) {
out = mxCreateDoubleMatrix( M, G, mxREAL );
z = mxGetPr( out );
} else {
if (D==0) {
z = (double*) mxCalloc( G, sizeof(double) );
} else {
z = (double*) mxCalloc( M*G, sizeof(double) );
}
out = mxCreateDoubleMatrix( B, G, mxREAL );
pout = mxGetPr( out );
out2 = mxCreateDoubleMatrix( B, 1, mxREAL );
pout2 = mxGetPr( out2 );
}
loopM = sizeM = M;
if (D==0) {
loopM = 1;
if (B>0)
sizeM = 1;
}
/* COMPUTE KDE */
/* LOOP THROUGH SOURCE (ENCODING) SPIKES */
for ( n=0; n<N; n++ ) {
/* LOOP THROUGH STIMULUS GRID */
for ( g=0; g<G; g++ ) {
/* INITIALIZE ACCUMULATORS */
acc_g_gauss[g] = 0;
acc_g_epa[g] = 0;
acc_g_delta[g] = 0;
acc_g_vm[g] = 0;
skip_g[g] = 0;
/* INITIALIZE INDICES */
idx1 = g;
idx2 = n;
/* LOOP THROUGH STIMULUS DIMENSIONS */
for ( q=0; q<Q; q++ ) {
/* GAUSSIAN KERNEL */
if (stimulus_kernel[q]==0) {
if (use_distance_lookup[q]) {
tmp = distance[q][ ((int) stimulus_grid[idx1])*NI[q] + (int)stimulus[idx2] ];
} else {
tmp = (stimulus_grid[idx1]-stimulus[idx2]);
}
acc_g_gauss[g] += tmp*tmp;
if (acc_g_gauss[g]>cutoff) {
skip_g[g] = 1;
break;
}
/* EPANECHNIKOV KERNEL */
} else if (stimulus_kernel[q]==1) {
if (use_distance_lookup[q]) {
tmp = distance[q][ ((int) stimulus_grid[idx1])*NI[q] + (int)stimulus[idx2] ];
} else {
tmp = (stimulus_grid[idx1]-stimulus[idx2]);
}
acc_g_epa[g]+=tmp*tmp;
if (acc_g_epa[g]>1) {
skip_g[g] = 1;
break;
}
/* VON MISES KERNEL */
} else if (stimulus_kernel[q]==2) {
if (use_distance_lookup[q]) {
tmp = distance[q][ ((int) stimulus_grid[idx1])*NI[q] + (int)stimulus[idx2] ];
} else {
tmp = fabs(stimulus_grid[idx1]-stimulus[idx2]);
}
if ( tmp<stimulus_vonmises[q] || tmp>(2*pi-stimulus_vonmises[q]) ) {
acc_g_vm[g] += stimulus_bandwidth[q] * cos(tmp);
} else {
skip_g[g] = 1;
break;
}
/* KRONECKER KERNEL */
} else {
if (use_distance_lookup[q]) {
tmp = distance[q][ ((int) stimulus_grid[idx1])*NI[q] + (int)stimulus[idx2] ];
} else {
tmp = (stimulus_grid[idx1]-stimulus[idx2]);
}
acc_g_delta[g] += tmp*tmp;
if (acc_g_delta[g]>1) {
skip_g[g] = 1;
break;
}
}
/* UPDATE INDICES */
idx1 += G;
idx2 += N;
}
}
/* LOOP THROUGH TEST (DECODING) SPIKES */
for ( m=0; m<loopM; m++ ) {
/* INITIALIZE ACCUMULATORS */
acc_a_gauss = 0;
acc_a_epa = 0;
acc_a_delta = 0;
acc_a_vm = 0;
/* INTIALIZE INDICES */
idx1 = m;
idx2 = n;
/* LOOP THROUGH RESPONSE DIMENSIONS */
for ( d=0; d<D; d++ ) {
/* GAUSSIAN KERNEL */
if (response_kernel[d]==0) {
tmp = (test_response[idx1]-response[idx2]);
acc_a_gauss += tmp*tmp;
if (acc_a_gauss>cutoff) {
goto nextm;
}
/* EPANECHNIKOV KERNEL */
} else if (response_kernel[d]==1) {
tmp = (test_response[idx1]-response[idx2]);
acc_a_epa += tmp*tmp;
if (acc_a_epa>1) {
goto nextm;
}
/* VON MISES KERNEL */
} else if (response_kernel[d]==2) {
tmp = fabs(test_response[idx1]-response[idx2]);
if ( tmp<response_vonmises[d] || tmp>(2*pi-response_vonmises[d]) ) {
acc_a_vm += response_bandwidth[d] * cos(tmp);
} else {
goto nextm;
}
/* KRONECKER KERNEL */
} else {
tmp = (test_response[idx1]-response[idx2]);
acc_a_delta += tmp*tmp;
if (acc_a_delta>1) {
goto nextm;
}
}
/* UPDATE INDICES */
idx1 += sizeM;
idx2 += N;
}
/* LOOP THROUGH STIMULUS GRID */
for ( g=0; g<G; g++ ) {
if (skip_g[g] || acc_g_gauss[g]+acc_a_gauss>cutoff || acc_g_epa[g]+acc_a_epa>1 || acc_g_delta[g]+acc_a_delta>1)
continue;
z[m+g*sizeM] += exp( -0.5*(acc_g_gauss[g]+acc_a_gauss) + acc_g_vm[g] + acc_a_vm ) * (1-acc_g_epa[g]-acc_a_epa);
}
nextm:
;
}
}
mxFree(acc_g_gauss);
mxFree(acc_g_epa);
mxFree(acc_g_delta);
mxFree(acc_g_vm);
mxFree(skip_g);
mxFree(stimulus_vonmises);
mxFree(response_vonmises);
if (argout!=NULL)
mxDestroyArray(argout);
mxDestroyArray(argin[0]);
mxDestroyArray(argin[1]);
/* compute log */
c1 = log(scaling_factor) - log((double)N);
if (B==0 && D==0) {
for (g=0;g<G;g++)
z[g*sizeM]=log( z[g*sizeM] + offset[g]*(double)N/scaling_factor ) + c1;
} else {
for (g=0; g<G; g++) {
idx = g*loopM;
c2 = offset[g]*(double)N/scaling_factor;
for (m=0; m<loopM ; m++ )
z[m+idx] = log( z[m+idx] + c2) + c1;
}
}
if (D==0 && B==0) { /* copy */
for (g=0; g<G; g++) {
idx = g*sizeM;
for (m=1; m<sizeM ; m++ )
z[m+idx] = z[idx];
}
}
if (B>0) {
next_idx = 0;
for (b=0; b<B; b++) {
while (next_idx<M && (timestamp[next_idx]<bins[b]))
next_idx++;
idx = next_idx;
while (idx<M && (timestamp[idx]<bins[b+B])) {
if (D>0) {
for (g=0; g<G; g++)
pout[b+g*B] += z[idx+g*M];
}
pout2[b]++;
idx++;
}
if (D==0) {
for (g=0; g<G; g++) {
pout[b+g*B] = pout2[b] * z[g*sizeM];
}
}
}
mxFree(z);
}
plhs[0] = out;
plhs[1] = out2;
}
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
int i, j, NS, NZB, count, bdim, match, domain, bindex, sindex, nzCounts=0;
int *observed, *bsubv, *ssubv, *bir, *sir, *bjc, *sjc, *mask, *ssize, *bcumprod, *scumprod;
double *pDomain, *pSize, *bpr, *spr;
mxArray *pTemp;
pTemp = mxGetField(prhs[0], 0, "CPT");
bpr = mxGetPr(pTemp);
bir = mxGetIr(pTemp);
bjc = mxGetJc(pTemp);
NZB = bjc[1];
pTemp = mxGetField(prhs[0], 0, "sizes");
pSize = mxGetPr(pTemp);
pDomain = mxGetPr(prhs[1]);
bdim = mxGetNumberOfElements(prhs[1]);
mask = malloc(bdim * sizeof(int));
ssize = malloc(bdim * sizeof(int));
observed = malloc(bdim * sizeof(int));
for(i=0; i<bdim; i++){
ssize[i] = (int)pSize[i];
}
count = 0;
for(i=0; i<bdim; i++){
domain = (int)pDomain[i] - 1;
pTemp = mxGetCell(prhs[2], domain);
if(pTemp){
mask[count] = i;
ssize[i] = 1;
observed[count] = (int)mxGetScalar(pTemp) - 1;
count++;
}
}
if(count == 0){
pTemp = mxGetField(prhs[0], 0, "CPT");
plhs[0] = mxDuplicateArray(pTemp);
free(mask);
free(ssize);
free(observed);
return;
}
bsubv = malloc(bdim * sizeof(int));
ssubv = malloc(count * sizeof(int));
bcumprod = malloc(bdim * sizeof(int));
scumprod = malloc(bdim * sizeof(int));
NS = 1;
for(i=0; i<bdim; i++){
NS *= ssize[i];
}
plhs[0] = mxCreateSparse(NS, 1, NS, mxREAL);
spr = mxGetPr(plhs[0]);
sir = mxGetIr(plhs[0]);
sjc = mxGetJc(plhs[0]);
sjc[0] = 0;
sjc[1] = NS;
bcumprod[0] = 1;
scumprod[0] = 1;
for(i=0; i<bdim-1; i++){
bcumprod[i+1] = bcumprod[i] * (int)pSize[i];
scumprod[i+1] = scumprod[i] * ssize[i];
}
nzCounts = 0;
for(i=0; i<NZB; i++){
bindex = bir[i];
ind_subv(bindex, bcumprod, bdim, bsubv);
for(j=0; j<count; j++){
ssubv[j] = bsubv[mask[j]];
}
match = 1;
for(j=0; j<count; j++){
if((ssubv[j]) != observed[j]){
match = 0;
break;
}
}
if(match){
spr[nzCounts] = bpr[i];
sindex = subv_ind(bdim, scumprod, bsubv);
sir[nzCounts] = sindex;
nzCounts++;
}
}
reset_nzmax(plhs[0], NS, nzCounts);
free(mask);
free(ssize);
free(observed);
free(bsubv);
free(ssubv);
free(bcumprod);
free(scumprod);
}
// Main function ===============================================================
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
const mxArray *A, *AC, *B, *BC;
int nA, nB, iA, iB, ASlen, *BSlenp, *BSlen, Rlen,
CaseSensitive = 1;
double *RA, *RAp, *RB, *RBp;
unsigned char **BS, **BSp, **BSEnd, *AS, *CaseArg;
// Check for proper number of arguments:
if (nrhs < 2 || nrhs > 3) {
mexErrMsgTxt("*** CStrAinBP[mex]: 2 or 3 inputs required.");
}
if (nlhs > 2) {
mexErrMsgTxt("*** CStrAinBP[mex]: 1 or 2 outputs allowed.");
}
// Set flag according to optional 3rd input:
if (nrhs == 3) {
// Compare first character of 3rd argument:
if (mxGetNumberOfElements(prhs[2]) > 0) {
CaseArg = (unsigned char *)mxGetData(prhs[2]);
if (*CaseArg == 'i' || *CaseArg == 'I') {
CaseSensitive = 0;
}
}
}
// Create a pointer to the input arrays:
A = prhs[0];
B = prhs[1];
// Check that inputs are cells:
if (!mxIsCell(A) || !mxIsCell(B)) {
mexErrMsgTxt("*** CStrAinBP[mex]: Inputs must be cells.");
}
// Get number of dimensions of the input string and cell:
nA = mxGetNumberOfElements(A);
nB = mxGetNumberOfElements(B);
// Create container for output arguments:
RA = (double *)mxMalloc(nA * sizeof(double));
RB = (double *)mxMalloc(nA * sizeof(double));
// Make list of pointers to elements of B and their length:
BSlen = (int *) mxMalloc(nB * sizeof(int));
BS = (unsigned char **)mxMalloc(nB * sizeof(unsigned char *));
BSEnd = BS + nB;
for (iB = 0, BSp = BS, BSlenp = BSlen; iB < nB; iB++) {
if ((BC = mxGetCell(B, iB)) == NULL) { // Uninitialized cell element:
mexErrMsgTxt("*** CStrAinBP[mex]: Element of B is NULL.");
}
if (!mxIsChar(BC)) {
mexErrMsgTxt("*** CStrAinBP[mex]: Element of B is no string.");
}
*BSlenp++ = mxGetNumberOfElements(BC);
*BSp++ = (unsigned char *)mxGetData(BC);
} // end for iB
// Pointers to list of strings:
RAp = RA;
RBp = RB;
if (CaseSensitive) { // -----------------------------------------------------
for (iA = 0; iA < nA; iA++) { // Loop over all strings of A:
if ((AC = mxGetCell(A, iA)) == NULL) { // Uninitialized cell element:
mexErrMsgTxt("*** CStrAinBP[mex]: Element of A is NULL.");
}
if (!mxIsChar(AC)) { // Check if cell element is a string:
mexErrMsgTxt("*** CStrAinBP[mex]: Element of A is no string.");
}
AS = (unsigned char *)mxGetData(AC);
ASlen = mxGetNumberOfElements(AC);
BSlenp = BSlen; // Pointer to list of lengths of B's strings
// Loop over pointers to strings of B:
for (BSp = BS; BSp < BSEnd; BSp++) {
if (ASlen == *BSlenp++) { // Cheap comparison of length
if (memcmp(AS, *BSp, ASlen * sizeof(mxChar)) == 0) {
*RAp++ = (double) (iA + 1);
*RBp++ = (double) (BSp - BS + 1);
break; // Just take first occurrence in B
}
}
} // end for BSp
} // end for iA
} else { // Not case-sensitive: ---------------------------------------------
// Same method except for memcmp -> my_memicmpW:
for (iA = 0; iA < nA; iA++) { // Loop over all strings of A:
if ((AC = mxGetCell(A, iA)) == NULL) { // Uninitialized cell element:
mexErrMsgTxt("*** CStrAinBP[mex]: Element of A is NULL.");
}
if (!mxIsChar(AC)) { // Check if cell element is a string:
mexErrMsgTxt("*** CStrAinBP[mex]: Element of A is no string.");
}
AS = (unsigned char *)mxGetData(AC);
ASlen = mxGetNumberOfElements(AC);
BSlenp = BSlen; // Pointer to list of lengths of B's strings
// Loop over pointers to strings of B:
for (BSp = BS; BSp < BSEnd; BSp++) {
if (ASlen == *BSlenp++) { // Cheap comparison of length
if (my_memicmpW(AS, *BSp, ASlen) == 0) {
*RAp++ = (double) (iA + 1);
*RBp++ = (double) (BSp - BS + 1);
break; // Just take first occurrence in B
}
}
} // end for BSp
} // end for iA
}
// Create output arguments, [0 x 0] for empty arrays:
Rlen = (int) (RAp - RA); // Number of found occurrences
plhs[0] = mxCreateDoubleMatrix(Rlen ? 1 : 0, Rlen, mxREAL);
memcpy(mxGetPr(plhs[0]), RA, Rlen * sizeof(double));
if (nlhs == 2) {
plhs[1] = mxCreateDoubleMatrix(Rlen ? 1 : 0, Rlen, mxREAL);
memcpy(mxGetPr(plhs[1]), RB, Rlen * sizeof(double));
}
// Free memory for indices, strings and strings lengths:
mxFree(RA);
mxFree(RB);
mxFree(BS);
mxFree(BSlen);
return;
}
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
// input arguments
GLuint programID = 0;
size_t nBuffers = 0;
size_t nNames = 0;
size_t nOffsets = 0;
size_t nIsNormalized = 0;
// input data
int i = 0;
GLuint attribIndex = 1;
mxArray* mxAttribName = NULL;
char* attribName = NULL;
double* mxOffsetData = NULL;
double* mxIsNormalizedData = NULL;
// VBO data
GLuint bufferID = 0;
size_t bytesPerElement = 0;
size_t byteOffset = 0;
GLint elementsPerVertex = 0;
GLsizei elementStride = 0;
GLsizei byteStride = 0;
mxArray* mxData = NULL;
GLenum glType = GL_FLOAT;
GLboolean isNormalized = GL_FALSE;
// status
GLint maxAttributes = -1;
size_t nSelected = 0;
int status = 0;
GLenum error = GL_NO_ERROR;
dotsMglClearGLErrors();
// empty input means disable all generic vertex attributes, exept 0
if (nrhs < 1 || mxIsEmpty(prhs[0])) {
glGetIntegerv(GL_MAX_VERTEX_ATTRIBS, &maxAttributes);
if (maxAttributes > 0) {
for (i=1; i<maxAttributes; i++)
glDisableVertexAttribArray(i);
}
plhs[0] = mxCreateDoubleScalar(0);
return;
}
// check input arguments
if (nrhs < 2 || nrhs > 5
|| !mxIsStruct(prhs[0]) || mxIsEmpty(prhs[0])
|| !mxIsStruct(prhs[1]) || mxIsEmpty(prhs[1])) {
plhs[0] = mxCreateDoubleScalar(-1);
usageError("dotsMglSelectVertexAttributes");
return;
}
// is this a shader program info struct?
programID = (GLuint)dotsMglGetInfoScalar(prhs[0], 0, "programID", &status);
if (status < 0) {
plhs[0] = mxCreateDoubleScalar(-2);
return;
}
// how many attribute buffers?
nBuffers = mxGetNumberOfElements(prhs[1]);
// how many attribute names?
if (nrhs >= 3 && mxIsCell(prhs[2]) && !mxIsEmpty(prhs[2])) {
nNames = mxGetNumberOfElements(prhs[2]);
if (nBuffers != nNames) {
mexPrintf("(dotsMglSelectVertexAttributes) Number of buffer names %d must match number of buffers %d.\n",
nNames, nBuffers);
plhs[0] = mxCreateDoubleScalar(-3);
return;
}
}
// how many buffer offsets?
if (nrhs >= 4 && mxIsDouble(prhs[3]) && !mxIsEmpty(prhs[3])) {
nOffsets = mxGetNumberOfElements(prhs[3]);
if (nBuffers != nOffsets) {
mexPrintf("(dotsMglSelectVertexAttributes) Number of buffer offsets %d must match number of buffers %d.\n",
nOffsets, nBuffers);
plhs[0] = mxCreateDoubleScalar(-4);
return;
}
mxOffsetData = mxGetPr(prhs[3]);
}
// how many buffer normalize flags?
if (nrhs >= 5 && mxIsDouble(prhs[4]) && !mxIsEmpty(prhs[4])) {
nIsNormalized = mxGetNumberOfElements(prhs[4]);
if (nBuffers != nIsNormalized) {
mexPrintf("(dotsMglSelectVertexAttributes) Number of buffer normalize flags %d must match number of buffers %d.\n",
nIsNormalized, nBuffers);
plhs[0] = mxCreateDoubleScalar(-5);
return;
}
mxIsNormalizedData = mxGetPr(prhs[4]);
}
// iterate buffers to enable attributes
for (i=0; i<nBuffers; i++) {
// enable the next numbered attribute
// ignoring attribute 0
attribIndex = i+1;
glEnableVertexAttribArray(attribIndex);
// assign a name to the numbered attribute?
if (nNames > 0){
mxAttribName = mxGetCell(prhs[2], i);
attribName = mxArrayToString(mxAttribName);
glBindAttribLocation(programID, attribIndex, (const GLchar*)attribName);
if (attribName != NULL){
mxFree(attribName);
attribName = NULL;
}
error = glGetError();
if(error != GL_NO_ERROR) {
mexPrintf("(dotsMglSelectVertexAttributes) Error assigning name %s to vertex attribute %d. glGetError()=%d\n",
attribName, attribIndex, error);
continue;
}
}
// VBO accounting
bufferID = (GLuint)dotsMglGetInfoScalar(prhs[1], i, "bufferID", &status);
if (status < 0) {
mexPrintf("(dotsMglSelectVertexAttributes) %dth buffer info struct is invalid.\n",
i);
continue;
}
// how are the VBO elements formatted?
elementsPerVertex = (GLint)dotsMglGetInfoScalar(prhs[1], i, "elementsPerVertex", &status);
elementStride = (GLsizei)dotsMglGetInfoScalar(prhs[1], i, "elementStride", &status);
bytesPerElement = (size_t)dotsMglGetInfoScalar(prhs[1], i, "bytesPerElement", &status);
byteStride = elementStride * bytesPerElement;
mxData = mxGetField(prhs[1], i, "mxData");
glType = dotsMglGetGLNumericType(mxData);
// use an offset into the VBO?
if (nOffsets > 0 && mxOffsetData != NULL)
byteOffset = (size_t)mxOffsetData[i] * bytesPerElement;
else
byteOffset = 0;
// normalize data in the VBO?
if (nIsNormalized > 0 && mxIsNormalizedData != NULL)
isNormalized = mxIsNormalizedData[i] ? GL_TRUE : GL_FALSE;
else
isNormalized = 0;
// assign the VBO to this numbered attribute
glBindBuffer(GL_ARRAY_BUFFER, bufferID);
glVertexAttribPointer(attribIndex,
elementsPerVertex,
glType,
isNormalized,
byteStride,
BUFFER_OFFSET(byteOffset));
glBindBuffer(GL_ARRAY_BUFFER, 0);
error = glGetError();
if(error != GL_NO_ERROR) {
mexPrintf("(dotsMglSelectVertexAttributes) Error selecting vertex %s data. glGetError()=%d\n",
attribName, error);
continue;
}
// success for this attribute
nSelected++;
}
// need to re-link the program when binding attribute names
if (nNames > 0){
glLinkProgram(programID);
error = glGetError();
if (error != GL_NO_ERROR) {
mexPrintf("(dotsMglSelectVertexAttributes) Could not link program. glGetError()=%d\n",
error);
plhs[0] = mxCreateDoubleScalar(-10);
return;
}
}
// success?
plhs[0] = mxCreateDoubleScalar(nSelected);
}
void LTFAT_NAME(ltfatMexFnc)( int nlhs, mxArray *plhs[],int nrhs, const mxArray *prhs[] )
{
#ifdef _DEBUG
static int atExitFncRegistered = 0;
if(!atExitFncRegistered)
{
LTFAT_NAME(ltfatMexAtExit)(LTFAT_NAME(tdMexAtExitFnc));
atExitFncRegistered = 1;
}
#endif
const mxArray* mxf = prhs[0];
const mxArray* mxg = prhs[1];
double* a = (double*) mxGetData(prhs[2]);
double* offset = (double*) mxGetData(prhs[3]);
char* ext = mxArrayToString(prhs[4]);
// input data length
mwSize L = mxGetM(mxf);
// number of channels
mwSize W = mxGetN(mxf);
// filter number
mwSize M = mxGetNumberOfElements(mxg);
// filter lengths
mwSize filtLen[M];
//mwSize* filtLen = mxMalloc(M*sizeof(mwSize));
for(unsigned int m=0;m<M;m++)
{
filtLen[m] = (mwSize) mxGetNumberOfElements(mxGetCell(mxg,m));
}
// output lengths
mwSize outLen[M];
//mwSize* outLen = mxMalloc(M*sizeof(mwSize));
if(!strcmp(ext,"per"))
{
for(unsigned int m = 0; m < M; m++)
{
outLen[m] = (mwSize) ceil( L/a[m] );
}
}
else if(!strcmp(ext,"valid"))
{
for(unsigned int m = 0; m < M; m++)
{
outLen[m] = (mwSize) ceil( (L-(filtLen[m]-1))/a[m] );
}
}
else
{
for(unsigned int m = 0; m < M; m++)
{
outLen[m] = (mwSize) ceil( (L + filtLen[m] - 1 + offset[m] )/a[m] );
}
}
// POINTER TO THE INPUT
LTFAT_TYPE* fPtr = (LTFAT_TYPE*) mxGetData(prhs[0]);
// POINTER TO THE FILTERS
LTFAT_TYPE* gPtrs[M];
// LTFAT_TYPE** gPtrs = (LTFAT_TYPE**) mxMalloc(M*sizeof(LTFAT_TYPE*));
for(mwIndex m=0;m<M;m++)
{
gPtrs[m] = (LTFAT_TYPE*) mxGetPr(mxGetCell(mxg, m));
}
// POINTER TO OUTPUTS
LTFAT_TYPE* cPtrs[M]; // C99 feature
//LTFAT_TYPE** cPtrs = (LTFAT_TYPE**) mxMalloc(M*sizeof(LTFAT_TYPE*));
plhs[0] = mxCreateCellMatrix(M, 1);
for(mwIndex m=0;m<M;++m)
{
mxSetCell(plhs[0], m, ltfatCreateMatrix(outLen[m], W,LTFAT_MX_CLASSID,LTFAT_MX_COMPLEXITY));
cPtrs[m] = (LTFAT_TYPE*) mxGetData(mxGetCell(plhs[0],m));
memset(cPtrs[m],0,outLen[m]*W*sizeof(LTFAT_TYPE));
}
// over all channels
// #pragma omp parallel for private(m)
for(mwIndex m =0; m<M; m++)
{
for(mwIndex w =0; w<W; w++)
{
// Obtain pointer to w-th column in input
LTFAT_TYPE *fPtrCol = fPtr + w*L;
// Obtaing pointer to w-th column in m-th element of output cell-array
LTFAT_TYPE *cPtrCol = cPtrs[m] + w*outLen[m];
//conv_td_sub(fPtrCol,L,&cPtrCol,outLen[m],(const double**)&gPtrs[m],filtLen[m],1,a[m],skip[m],ltfatExtStringToEnum(ext),0);
LTFAT_NAME(convsub_td)(fPtrCol,L,cPtrCol,outLen[m],gPtrs[m],filtLen[m],a[m],-offset[m],ltfatExtStringToEnum(ext));
}
}
}
void recurse_object(const mxArray* in, json& obj)
{
// Go over all types
if (mxIsCell(in)) {
int N = mxGetNumberOfElements(in);
for (int a = 0; a < N; ++a) {
obj.emplace_back();
recurse_object(mxGetCell(in, a), obj.back());
}
} else if (mxIsStruct(in)) {
int M = mxGetNumberOfFields(in);
std::vector<const char*> fnames(M);
for (int b = 0; b < M; ++b)
fnames[b] = mxGetFieldNameByNumber(in, b);
int N = mxGetNumberOfElements(in);
for (int a = 0; a < N; ++a) {
json obj_;
for (int b = 0; b < M; ++b)
recurse_object(mxGetFieldByNumber(in, a, b), obj_[fnames[b]]);
if (N == 1)
obj = std::move(obj_);
else
obj.push_back(std::move(obj_));
}
} else if (mxIsChar(in)) {
obj = json::parse(mxArrayToString(in));
} else if (mxIsLogical(in)) {
int N = mxGetNumberOfElements(in);
const mxLogical* data = (const mxLogical*)mxGetData(in);
if (N == 1) {
obj = data[0] != 0;
} else {
for (int a = 0; a < N; ++a)
obj.push_back(data[a] != 0);
}
} else if (mxIsNumeric(in)) {
int N = mxGetNumberOfElements(in);
const void* data = (const void*)mxGetData(in);
switch (mxGetClassID(in)) {
case mxDOUBLE_CLASS:
if (N == 1) { obj = ((const double*)data)[0]; } else {
for (int a = 0; a < N; ++a) obj.push_back(((const double*)data)[a]); }
break;
case mxSINGLE_CLASS:
if (N == 1) { obj = ((const float*)data)[0]; } else {
for (int a = 0; a < N; ++a) obj.push_back(((const float*)data)[a]); }
break;
case mxUINT8_CLASS:
if (N == 1) { obj = ((const uint8_t*)data)[0]; } else {
for (int a = 0; a < N; ++a) obj.push_back(((const uint8_t*)data)[a]); }
break;
case mxINT8_CLASS:
if (N == 1) { obj = ((const int8_t*)data)[0]; } else {
for (int a = 0; a < N; ++a) obj.push_back(((const int8_t*)data)[a]); }
break;
case mxUINT16_CLASS:
if (N == 1) { obj = ((const uint16_t*)data)[0]; } else {
for (int a = 0; a < N; ++a) obj.push_back(((const uint16_t*)data)[a]); }
break;
case mxINT16_CLASS:
if (N == 1) { obj = ((const int16_t*)data)[0]; } else {
for (int a = 0; a < N; ++a) obj.push_back(((const int16_t*)data)[a]); }
break;
case mxUINT32_CLASS:
if (N == 1) { obj = ((const uint32_t*)data)[0]; } else {
for (int a = 0; a < N; ++a) obj.push_back(((const uint32_t*)data)[a]); }
break;
case mxINT32_CLASS:
if (N == 1) { obj = ((const int32_t*)data)[0]; } else {
for (int a = 0; a < N; ++a) obj.push_back(((const int32_t*)data)[a]); }
break;
case mxUINT64_CLASS:
if (N == 1) { obj = ((const uint64_t*)data)[0]; } else {
for (int a = 0; a < N; ++a) obj.push_back(((const uint64_t*)data)[a]); }
break;
case mxINT64_CLASS:
if (N == 1) { obj = ((const int64_t*)data)[0]; } else {
for (int a = 0; a < N; ++a) obj.push_back(((const int64_t*)data)[a]); }
break;
default:
mexErrMsgTxt("Unsupported type.");
break;
}
} else {
mexErrMsgTxt("Unrecognized type.");
}
}
/*
%COMP_IFILTERBANK_TD Synthesis filterbank
% Usage: f=comp_ifilterbank_fft(c,g,a,Ls,offset,ext);
%
% Input parameters:
% c : Cell array of length M, each element is N(m)*W matrix.
% g : Filterbank filters - length M cell-array, each element is vector of length filtLen(m)
% a : Upsampling factors - array of length M.
% offset : Delay of the filters - scalar or array of length M.
% Ls : Output length.
% ext : Border exension technique.
%
% Output parameters:
% f : Output Ls*W array.
%
*/
void LTFAT_NAME(ltfatMexFnc)( int nlhs, mxArray *plhs[],int nrhs, const mxArray *prhs[] )
{
// printf("Filename: %s, Function name %s, %d \n.",__FILE__,__func__,mxIsDouble(prhs[0]));
const mxArray* mxc = prhs[0];
const mxArray* mxg = prhs[1];
double* a = mxGetPr(prhs[2]);
double* Lsdouble = mxGetPr(prhs[3]);
unsigned int Ls = (unsigned int) *Lsdouble;
double* offset = mxGetPr(prhs[4]);
char* ext = mxArrayToString(prhs[5]);
// number of channels
unsigned int W = mxGetN(mxGetCell(mxc,0));
// filter number
unsigned int M = mxGetNumberOfElements(mxg);
// input data length
unsigned int* Lc = mxMalloc(M*sizeof(unsigned int));
for(unsigned int m=0;m<M;m++)
{
Lc[m] = (unsigned int) mxGetM(mxGetCell(mxc,m));
}
// filter lengths
unsigned int* filtLen = mxMalloc(M*sizeof(unsigned int));
for(unsigned int m=0;m<M;m++)
{
filtLen[m] = (unsigned int) mxGetNumberOfElements(mxGetCell(mxg,m));
}
// POINTER TO THE INPUT
LTFAT_TYPE** cPtrs = (LTFAT_TYPE**) mxMalloc(M*sizeof(LTFAT_TYPE*));
for(unsigned int m=0;m<M;++m)
{
cPtrs[m] = (LTFAT_TYPE*) mxGetData(mxGetCell(mxc,m));
}
// allocate output
plhs[0] = ltfatCreateMatrix(Ls, W,LTFAT_MX_CLASSID,LTFAT_MX_COMPLEXITY);
// POINTER TO OUTPUT
LTFAT_TYPE* fPtr = (LTFAT_TYPE*) mxGetData(plhs[0]);
// Set to zeros
memset(fPtr,0,Ls*W*sizeof(LTFAT_TYPE));
// POINTER TO THE FILTERS
LTFAT_TYPE** gPtrs = (LTFAT_TYPE**) mxMalloc(M*sizeof(LTFAT_TYPE*));
for(unsigned int m=0;m<M;m++)
{
gPtrs[m] = (LTFAT_TYPE*) mxGetData(mxGetCell(mxg, m));
}
// over all channels
// #pragma omp parallel for private(m)
for(unsigned int m =0; m<M; m++)
{
for(unsigned int w =0; w<W; w++)
{
// Obtain pointer to w-th column in input
LTFAT_TYPE *fPtrCol = fPtr + w*Ls;
// Obtaing pointer to w-th column in m-th element of output cell-array
LTFAT_TYPE *cPtrCol = cPtrs[m] + w*Lc[m];
//(upconv_td)(const LTFAT_TYPE *in, int inLen, LTFAT_TYPE *out, const int outLen, const LTFAT_TYPE *filts, int fLen, int up, int skip, enum ltfatWavExtType ext)
LTFAT_NAME(upconv_td)(cPtrCol,Lc[m],fPtrCol,Ls,gPtrs[m],filtLen[m],a[m],-offset[m],ltfatExtStringToEnum(ext));
}
}
}
MVT_3D_Object::MVT_3D_Object(ENUM_OBJECT_CATEGORY object_category, const char* filepath_3dobject_model)
{
m_object_category = object_category;
MATFile* mat = matOpen(filepath_3dobject_model,"r");
if( mat != NULL )
{
mxArray* pmxCad = matGetVariable(mat, "cad");
pmxCad = mxGetCell(pmxCad,0);
/*
* Names of parts
*/
mxArray* pmxNames = mxGetField(pmxCad, 0, "pnames");
m_num_of_partsNroots = mxGetNumberOfElements(pmxNames);
for( unsigned int i=0; i<m_num_of_partsNroots; i++)
{
mxArray* pmxName = mxGetCell(pmxNames, i);
m_names_partsNroots.push_back(MxArray(pmxName).toString());
}
/*
* Parts2d_Front
*/
mxArray* pmxPars2d_front = mxGetField(pmxCad, 0, "parts2d_front");
for( unsigned int i=0; i<m_num_of_partsNroots; i++)
{
MVT_2D_Part_Front front;
front.width = MxArray(mxGetField(pmxPars2d_front, i, "width" )).toDouble();
front.height = MxArray(mxGetField(pmxPars2d_front, i, "height" )).toDouble();
front.distance = MxArray(mxGetField(pmxPars2d_front, i, "distance")).toDouble();
cv::Mat mat_tmp = MxArray(mxGetField(pmxPars2d_front, i, "vertices")).toMat();
unsigned int n_row = mat_tmp.rows;
for( unsigned int r=0; r<n_row ; r++)
{
front.vertices.push_back(cv::Point2d(mat_tmp.at<double>(r,0), mat_tmp.at<double>(r,1)));
}
front.center = MxArray(mxGetField(pmxPars2d_front, i, "center")).toPoint_<double>();
front.viewport = MxArray(mxGetField(pmxPars2d_front, i, "viewport")).toDouble();
front.name = MxArray(mxGetField(pmxPars2d_front, i, "pname")).toString();
m_2dparts_front.push_back(front);
}
/*
* Part
*/
mxArray* pmxParts = mxGetField(pmxCad, 0, "parts");
m_num_of_parts = mxGetNumberOfElements(pmxParts);
for( unsigned int i=0 ; i<m_num_of_parts; i++ )
{
MVT_3D_Part part;
/* Vertices */
mxArray* mxVertices = mxGetField(pmxParts, i, "vertices");
cv::Mat matVertices = MxArray(mxVertices).toMat();
unsigned int n_rows = matVertices.rows;
for( unsigned int r=0; r<n_rows; r++)
{
cv::Mat matTmp = matVertices.row(r);
part.vertices.push_back
(
cv::Point3d( matTmp.at<double>(0),
matTmp.at<double>(1),
matTmp.at<double>(2) )
);
}
/* plane */
MxArray MxPlane(mxGetField(pmxParts, i, "plane"));
for( int j=0 ; j<4; j++ )
{
part.plane[j] = MxPlane.at<double>(j);
}
/* center */
MxArray MxCenter(mxGetField(pmxParts, i, "center"));
part.center.x = MxCenter.at<double>(0);
part.center.y = MxCenter.at<double>(1);
part.center.z = MxCenter.at<double>(2);
/* xaxis */
MxArray MxXAxis(mxGetField(pmxParts, i, "xaxis"));
part.xaxis.x = MxXAxis.at<double>(0);
part.xaxis.y = MxXAxis.at<double>(1);
part.xaxis.z = MxXAxis.at<double>(2);
/* yaxis */
MxArray MxYAxis(mxGetField(pmxParts, i, "yaxis"));
part.yaxis.x = MxYAxis.at<double>(0);
part.yaxis.y = MxYAxis.at<double>(1);
part.yaxis.z = MxYAxis.at<double>(2);
m_3dparts.push_back(part);
/*
* Occlusion Information
*/
mxArray* pmxAzimuth = mxGetField(pmxCad, 0, "azimuth" );
m_disc_azimuth = MxArray(pmxAzimuth).toVector<MVT_AZIMUTH>();
mxArray* pmxElevation = mxGetField(pmxCad, 0, "elevation" );
m_disc_elevation = MxArray(pmxElevation).toVector<MVT_ELEVATION>();
mxArray* pmxDistance = mxGetField(pmxCad, 0, "distance" );
m_disc_distance = MxArray(pmxDistance).toVector<MVT_DISTANCE>();
mxArray* pmxParts2d = mxGetField(pmxCad, 0, "parts2d");
m_num_of_disc_azimuth = m_disc_azimuth.size();
m_num_of_disc_elevation = m_disc_elevation.size();
m_num_of_disc_distance = m_disc_distance.size();
m_is_occluded = new bool***[m_num_of_disc_azimuth];
for( unsigned int a=0; a<m_num_of_disc_azimuth; a++ )
{
m_is_occluded[a] = new bool**[m_num_of_disc_elevation];
for( unsigned int e=0; e<m_num_of_disc_elevation; e++ )
{
m_is_occluded[a][e] = new bool*[m_num_of_disc_distance];
for( unsigned int d=0; d<m_num_of_disc_distance; d++ )
{
m_is_occluded[a][e][d] = new bool[m_num_of_partsNroots];
unsigned int idx = m_num_of_disc_distance*m_num_of_disc_elevation*a +
m_num_of_disc_distance*e +
d;
for( unsigned int p=0; p<m_num_of_partsNroots; p++)
{
mxArray* pmxPart = mxGetField(pmxParts2d, idx, m_names_partsNroots[p].c_str());
m_is_occluded[a][e][d][p] = mxIsEmpty(pmxPart);
}
}
}
}
}
mxDestroyArray(pmxCad);
matClose(mat);
}
}
void mexFunction( int nlhs, mxArray *plhs[],int nrhs, const mxArray *prhs[] )
{
if(nrhs < 4 || nrhs > 5)
mexErrMsgTxt("Improper number of input arguments.\n\n"
"ARGMAX_MEX estimates the position of landmarks.\n\n"
"Synopsis: \n"
" [ \\hat{s} ]= argmax_mex(options, W, mapTable, lbp [, L]) \n"
"\n"
" Input: \n"
" options [1 x 1 structure] detector options\n"
" W [n x 1 (double)] joint parameter vector\n"
" mapTable [M x 4 (double)] mapping table for joint parameter vector W\n"
" lbp [1 x M (cell)] LBP sparse features\n"
" L [M x 1 (cell)] precomputed losses, optional parameter (for learning stage)\n"
" Output: \n"
" \\hat{s} [M x 2 (double)] estimated landmark positions\n");
//--------------------------------------------------------------------------
// Load input
double * W;
uint32_t W_ROWS, W_COLS;
FLANDMARK_Options options;
uint8_t M;
const mwSize *dims;
double * tmp_ptr;
mxArray *tmp_field_ptr, *cell_ptr;
mxArray * psigs0 = mxGetField(prhs[0], 0, "PsiGS0");
dims = mxGetDimensions(psigs0);
options.PSIG_ROWS[0] = dims[0];
options.PSIG_COLS[0] = dims[1];
mxArray * psigs1 = mxGetField(prhs[0], 0, "PsiGS1");
dims = mxGetDimensions(psigs1);
options.PSIG_ROWS[1] = dims[0];
options.PSIG_COLS[1] = dims[1];
mxArray * psigs2 = mxGetField(prhs[0], 0, "PsiGS2");
dims = mxGetDimensions(psigs2);
options.PSIG_ROWS[2] = dims[0];
options.PSIG_COLS[2] = dims[1];
int tsize = -1, rows = -1, cols = -1;
double * result;
bool lossy = (nrhs > 4) ? true : false;
// options ----------------------------------------------------------------
//options.M = 7;
tmp_field_ptr = mxGetField(prhs[0], 0, "M");
tmp_ptr = (double*)mxGetPr(tmp_field_ptr);
options.M = (int)tmp_ptr[0];
M = options.M;
//int mapTable[7*4];
int * mapTable = (int*)calloc(M*4, sizeof(int));
options.S = (int*)calloc(4*M, sizeof(int));
// options.S ---------------------------------------------------
tmp_field_ptr = mxGetField(prhs[0], 0, "S");
dims = mxGetDimensions(tmp_field_ptr);
tmp_ptr = (double*)mxGetPr(tmp_field_ptr);
for (int i = 0; i < 4*options.M; ++i)
{
options.S[i] = (int)tmp_ptr[i];
}
// W ----------------------------------------------------------------------
dims = mxGetDimensions(prhs[1]);
W_ROWS = dims[0]; W_COLS = dims[1];
bool WisSparse = mxIsSparse(prhs[1]);
if (WisSparse)
{
W = (double*)calloc(W_ROWS*W_COLS, sizeof(double));
double * pr = (double*)mxGetPr(prhs[1]);
mwIndex * ir = mxGetIr(prhs[1]);
mwSize nzmax = mxGetNzmax(prhs[1]);
for (int ii = 0; ii < nzmax; ++ii)
{
W[ir[ii]] = pr[ii];
}
} else {
W = (double*)mxGetPr(prhs[1]);
}
// ------------------------------------------------------------------------
// mapTable
tmp_ptr = (double*)mxGetPr(prhs[2]);
dims = mxGetDimensions(prhs[2]);
if (dims[0]*dims[1] != M*4)
{
mexErrMsgTxt("mapTable must be a matrix [M x 4 (double)]");
}
for (int i = 0; i < M*4; ++i)
{
mapTable[i] = (int)tmp_ptr[i];
}
// prepare output matrix
plhs[0] = mxCreateNumericMatrix(2, M, mxDOUBLE_CLASS, mxREAL);
result = (double*)mxGetPr(plhs[0]);
//--------------------------------------------------------------------------
// get Q, G
double ** q = (double**)calloc(M, sizeof(double*));
double ** g = (double**)calloc((M-1), sizeof(double*));
int idx_qtemp = 0;
double * L;
for (int idx = 0; idx < M; ++idx)
{
// Q
tsize = mapTable[INDEX(idx, 1, M)] - mapTable[INDEX(idx, 0, M)] + 1;
double * q_temp = (double*)calloc(tsize, sizeof(double));
memcpy(q_temp, W+mapTable[INDEX(idx, 0, M)]-1, tsize*sizeof(double));
// sparse dot product <W_q, PSI_q>
cell_ptr = mxGetCell(prhs[3], idx);
dims = mxGetDimensions(cell_ptr);
cols = dims[1];
rows = dims[0];
uint32_t *psi_temp = (uint32_t*)mxGetPr(cell_ptr);
if (lossy)
{
L = (double*)mxGetPr(mxGetCell(prhs[4], idx));
}
q[idx] = (double*)malloc(cols*sizeof(double));
for (int i = 0; i < cols; ++i)
{
double dotprod = 0.0f;
for (int j = 0; j < rows; ++j)
{
idx_qtemp = psi_temp[(rows*i) + j];
dotprod += q_temp[ idx_qtemp ];
}
q[idx][i] = dotprod;
if (lossy)
{
q[idx][i] += L[i];
}
}
free(q_temp);
// G
if (idx > 0)
{
tsize = mapTable[INDEX(idx, 3, M)] - mapTable[INDEX(idx, 2, M)] + 1;
g[idx - 1] = (double*)malloc(tsize*sizeof(double));
memcpy(g[idx - 1], W+mapTable[INDEX(idx, 2, M)]-1, tsize*sizeof(double));
}
}
// compute argmax
int * indices = (int*)malloc(M*sizeof(int));
tsize = mapTable[INDEX(1, 3, M)] - mapTable[INDEX(1, 2, M)] + 1;
// left branch - store maximum and index of s5 for all positions of s1
dims = mxGetDimensions(mxGetCell(prhs[3], 1));
int q1_length = dims[1];
double * s1 = (double *)calloc(2*q1_length, sizeof(double));
double * s1_maxs = (double *)calloc(q1_length, sizeof(double));
for (int i = 0; i < q1_length; ++i)
{
// dot product <g_5, PsiGS1>
dims = mxGetDimensions(mxGetCell(psigs1, INDEX(i, 0, options.PSIG_ROWS[1])));
maximize_gdotprod(
&s1[INDEX(0, i, 2)], &s1[INDEX(1, i, 2)],
q[5], g[4], (double*)mxGetPr(mxGetCell(psigs1, INDEX(i, 0, options.PSIG_ROWS[1]))),
dims[1], tsize);
s1[INDEX(0, i, 2)] += q[1][i];
}
for (int i = 0; i < q1_length; ++i)
{
s1_maxs[i] = s1[INDEX(0, i, 2)];
}
// right branch (s2->s6) - store maximum and index of s6 for all positions of s2
dims = mxGetDimensions(mxGetCell(prhs[3], 2));
int q2_length = dims[1];
double * s2 = (double *)calloc(2*q2_length, sizeof(double));
double * s2_maxs = (double *)calloc(q2_length, sizeof(double));
for (int i = 0; i < q2_length; ++i)
{
// dot product <g_6, PsiGS2>
dims = mxGetDimensions(mxGetCell(psigs2, INDEX(i, 0, options.PSIG_ROWS[2])));
maximize_gdotprod(
&s2[INDEX(0, i, 2)], (double*)&s2[INDEX(1, i, 2)],
q[6], g[5], (double*)mxGetPr(mxGetCell(psigs2, INDEX(i, 0, options.PSIG_ROWS[2]))),
dims[1], tsize);
s2[INDEX(0, i, 2)] += q[2][i];
}
for (int i = 0; i < q2_length; ++i)
{
s2_maxs[i] = s2[INDEX(0, i, 2)];
}
// the root s0 and its connections
dims = mxGetDimensions(mxGetCell(prhs[3], 0));
int q0_length = dims[1];
double maxs0 = -FLT_MAX;
int maxs0_idx = -1;
double maxq10 = -FLT_MAX, maxq20 = -FLT_MAX, maxq30 = -FLT_MAX, maxq40 = -FLT_MAX,
maxq70 = -FLT_MAX;
double * s0 = (double *)calloc(M*q0_length, sizeof(double));
for (int i = 0; i < q0_length; ++i)
{
// q10
maxq10 = -FLT_MAX;
dims = mxGetDimensions(mxGetCell(psigs0, INDEX(i, 0, options.PSIG_ROWS[0])));
maximize_gdotprod(
&maxq10, &s0[INDEX(1, i, M)],
s1_maxs, g[0], (double*)mxGetPr(mxGetCell(psigs0, INDEX(i, 0, options.PSIG_ROWS[0]))),
dims[1], tsize);
s0[INDEX(5, i, M)] = s1[INDEX(1, (int)s0[INDEX(1, i, M)], 2)];
// q20
maxq20 = -FLT_MAX;
dims = mxGetDimensions(mxGetCell(psigs0, INDEX(i, 1, options.PSIG_ROWS[0])));
maximize_gdotprod(
&maxq20, &s0[INDEX(2, i, M)],
s2_maxs, g[1], (double*)mxGetPr(mxGetCell(psigs0, INDEX(i, 1, options.PSIG_ROWS[0]))),
dims[1], tsize);
s0[INDEX(6, i, M)] = s2[INDEX(1, (int)s0[INDEX(2, i, M)], 2)];
// q30
maxq30 = -FLT_MAX;
dims = mxGetDimensions(mxGetCell(psigs0, INDEX(i, 2, options.PSIG_ROWS[0])));
maximize_gdotprod(
&maxq30, &s0[INDEX(3, i, M)],
q[3], g[2], (double*)mxGetPr(mxGetCell(psigs0, INDEX(i, 2, options.PSIG_ROWS[0]))),
dims[1], tsize);
// q40
maxq40 = -FLT_MAX;
dims = mxGetDimensions(mxGetCell(psigs0, INDEX(i, 3, options.PSIG_ROWS[0])));
maximize_gdotprod(
&maxq40, &s0[INDEX(4, i, M)],
q[4], g[3], (double*)mxGetPr(mxGetCell(psigs0, INDEX(i, 3, options.PSIG_ROWS[0]))),
dims[1], tsize);
// q70
maxq70 = -FLT_MAX;
dims = mxGetDimensions(mxGetCell(psigs0, INDEX(i, 4, options.PSIG_ROWS[0])));
maximize_gdotprod(
&maxq70, &s0[INDEX(7, i, M)],
q[7], g[6], (double*)mxGetPr(mxGetCell(psigs0, INDEX(i, 4, options.PSIG_ROWS[0]))),
dims[1], tsize);
// sum q10+q20+q30+q40+q70
if (maxs0 < maxq10+maxq20+maxq30+maxq40+maxq70+q[0][i])
{
maxs0_idx = i;
s0[INDEX(0, i, M)] = i;
maxs0 = maxq10+maxq20+maxq30+maxq40+maxq70+q[0][i];
}
}
// get indices
for (int i = 0; i < M; ++i)
{
indices[i] = (int)s0[INDEX(0, maxs0_idx, M)+i]+1;
}
// cleanup temp variables
free(s0);
free(s1); free(s1_maxs);
free(s2); free(s2_maxs);
// cleanup W if it was created
if (WisSparse)
{
free(W);
}
// cleanup q
for (int i = 0; i < M; ++i)
{
free(q[i]);
}
free(q);
// cleanup g
for (int i = 0; i < M - 1; ++i)
{
free(g[i]);
}
free(g);
// convert 1D indices to 2D coordinates of estimated positions
int * optionsS = &options.S[0];
for (int i = 0; i < M; ++i)
{
int rows = optionsS[INDEX(3, i, 4)] - optionsS[INDEX(1, i, 4)] + 1;
result[INDEX(0, i, 2)] = COL(indices[i], rows) + optionsS[INDEX(0, i, 4)];
result[INDEX(1, i, 2)] = ROW(indices[i], rows) + optionsS[INDEX(1, i, 4)];
}
free(indices);
free(options.S);
free(mapTable);
return;
}
static PyObject* mat2py(const mxArray *a) {
size_t ndims = mxGetNumberOfDimensions(a);
const mwSize *dims = mxGetDimensions(a);
mxClassID cls = mxGetClassID(a);
size_t nelem = mxGetNumberOfElements(a);
char *data = (char*) mxGetData(a);
char *imagData = (char*) mxGetImagData(a);
if (debug) mexPrintf("cls = %d, nelem = %d, ndims = %d, dims[0] = %d, dims[1] = %d\n", cls, nelem, ndims, dims[0], dims[1]);
if (cls == mxCHAR_CLASS) {
char *str = mxArrayToString(a);
PyObject *o = PyString_FromString(str);
mxFree(str);
return o;
} else if (mxIsStruct(a)) {
PyObject *o = PyDict_New();
PyObject *list;
PyObject *pyItem;
mxArray *item;
int i, j;
const char *fieldName;
int nfields = mxGetNumberOfFields(a);
if (debug) mexPrintf("nfields = %d, nelem = %d\n", nfields, nelem);
for(i = 0; i < nfields; i++) {
fieldName = mxGetFieldNameByNumber(a, i);
list = PyList_New(nelem);
for(j = 0; j < nelem; j++) {
item = mxGetFieldByNumber(a, j, i);
if(item == NULL)
{
Py_DECREF(list);
Py_DECREF(o);
mexErrMsgIdAndTxt("matpy:NullFieldValue", "Null field in struct");
}
pyItem = mat2py(item);
if(pyItem == NULL)
{
Py_DECREF(list);
Py_DECREF(o);
mexErrMsgIdAndTxt("matpy:UnsupportedVariableType", "Unsupported variable type in struct");
}
PyList_SetItem(list, j, pyItem);
}
PyDict_SetItemString(o, fieldName, list);
}
Py_DECREF(list);
return o;
}
PyObject *list = PyList_New(nelem);
const char *dtype = NULL;
if (mxIsCell(a))
{
dtype = "object";
for (int i = 0; i < nelem; i++)
{
PyObject *item = mat2py(mxGetCell(a, i));
if(NULL != item)
{
PyList_SetItem(list, i, item);
}
else // Failure
{
Py_DECREF(list);
mexErrMsgIdAndTxt("matpy:UnsupportedVariableType", "Unsupported variable type in a cell");
}
}
return list;
} else {
if (imagData == NULL) {
#define CASE(cls,c_type,d_type,py_ctor) case cls: for (int i = 0; i < nelem; i++) { \
dtype=d_type; \
PyObject *item = py_ctor(*((c_type*) data)); \
if (debug) mexPrintf("Setting %d to %f (item = 0x%08X)\n", i, (double) *((c_type*) data), item); \
data += sizeof(c_type); \
if (PyList_SetItem(list, i, item) == -1) PyErr_Print(); } \
break
switch(cls) {
CASE(mxLOGICAL_CLASS, bool, "bool", PyBool_FromLong);
CASE(mxDOUBLE_CLASS, double, "float64", PyFloat_FromDouble);
CASE(mxSINGLE_CLASS, float, "float32", PyFloat_FromDouble);
CASE(mxINT8_CLASS, char, "int8", PyInt_FromLong);
CASE(mxUINT8_CLASS, unsigned char, "uint8", PyInt_FromLong);
CASE(mxINT16_CLASS, short, "int16", PyInt_FromLong);
CASE(mxUINT16_CLASS, unsigned short, "uint16", PyInt_FromLong);
CASE(mxINT32_CLASS, int, "int32", PyInt_FromLong);
CASE(mxUINT32_CLASS, unsigned int, "uint32", PyLong_FromLongLong);
CASE(mxINT64_CLASS, long long, "int64", PyLong_FromLongLong);
CASE(mxUINT64_CLASS, unsigned long long, "uint64", PyLong_FromUnsignedLongLong);
default:
mexErrMsgIdAndTxt("matpy:UnsupportedVariableType", "Unsupported variable type");
}
} else {
#undef CASE
#define CASE(cls,c_type,d_type) case cls: for (int i = 0; i < nelem; i++) { \
dtype = d_type; \
PyObject *item = PyComplex_FromDoubles(*((c_type*) data), *((c_type*) imagData)); \
data += sizeof(c_type); \
imagData += sizeof(c_type); \
PyList_SetItem(list, i, item); } \
break
switch(cls) {
CASE(mxDOUBLE_CLASS, double, "complex128");
CASE(mxSINGLE_CLASS, float, "complex64");
CASE(mxINT8_CLASS, char, "complex64");
CASE(mxUINT8_CLASS, unsigned char, "complex64");
CASE(mxINT16_CLASS, short, "complex64");
CASE(mxUINT16_CLASS, unsigned short, "complex64");
CASE(mxINT32_CLASS, int, "complex128");
CASE(mxUINT32_CLASS, unsigned int, "complex128");
CASE(mxINT64_CLASS, long long, "complex128");
CASE(mxUINT64_CLASS, unsigned long long, "complex128");
default:
mexErrMsgIdAndTxt("matpy:UnsupportedVariableType", "Unsupported variable type");
}
}
}
//usage:feature = feaGen( training,depth,ndim);
//state:finishing
//version:v1
//notation: maximum size of buffer is 1024
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, mxArray * prhs[])
{
// check the input parameter
if (nlhs != 1)
mexErrMsgTxt(" error in using feaGen, one output is needed");
if (nrhs != 3)
mexErrMsgTxt(" error in using feaGen, three input are needed");
if (!mxIsCell(prhs[0]))
{
mexErrMsgTxt(" input type error");
}
mxArray * pp, *ptemp;
mwSize M;
mwSize depth, ndim;
int i, j, k, m, n, intTemp;
double *pointer;
//get parameter
depth = mxGetScalar(prhs[1]);
ndim = mxGetScalar(prhs[2]);
M = mxGetM(prhs[0]);
//alloc the space
char *buf = (char*) mxMalloc((unsigned int) (MAXSIZE) * sizeof(char));
char ** fea;
fea = (char**) mxMalloc((unsigned int) ndim * sizeof(char*));
for (i = 0; i < ndim; i++)
{
fea[i] = (char*) mxMalloc((unsigned int) (MAXSIZE) * sizeof(char));
}
feature fv(ndim, depth, M);
for (i = 0; i < M; i++)
{
fv.addLine();
ptemp = mxGetCell(prhs[0], i);
if (mxGetString(ptemp, buf, (unsigned int) MAXSIZE))
mexErrMsgTxt("error in the buffer of this function:line53");
#ifdef debug
mexPrintf("%s",buf);
#endif
for (j = 0; buf[j] != '\0'; j++)
{
intTemp = char2num(buf[j]);
for (int l = 0; l < ndim; l++)
{
fea[l][j] = (int)(intTemp & 0x1) + '0';
intTemp >>= 1;
}
}
int len = j;
#ifdef debug
mexPrintf("%s",len);
#endif
char *temp;
temp = (char*) mxMalloc((ndim * depth + 1) * sizeof(char));
for (j = 0; j <= len - depth; j++)
{
intTemp = 0;
int mm, nn;
for (nn = 0; nn < ndim; nn++)
{
for (mm = 0; mm < depth; mm++)
{
temp[intTemp++] = fea[nn][mm + j];
}
}
*(temp + ndim * depth) = '\0';
intTemp = ndim * depth;
int index = to2num(temp, intTemp);
if( index < 0 || index > power2(ndim,depth))
{
mexErrMsgTxt("error in input format line:90");
}
fv.store(index);
}
mxFree(temp);
}
mxFree(buf);
for (i = 0; i < ndim; i++)
{
mxFree(fea[i]);
}
mxFree(fea);
int lineSize = fv.getLineSize();
plhs[0] = mxCreateDoubleMatrix(fv.getLen(), lineSize, mxREAL);
pointer = mxGetPr(plhs[0]);
fv.transaction(pointer);
}
void
mexFunction(int nlhs, mxArray * plhs[], int nrhs, const mxArray * prhs[]) {
char *filename;
FILE *dta_file;
int ret = 0;
filename = (char *)malloc(1 + mxGetN(prhs[0]));
mxGetString(prhs[0], filename, 1 + mxGetN(prhs[0]));
char *ws = (char *)malloc(1 + mxGetN(prhs[3]));
mxGetString(prhs[3], ws, 1 + mxGetN(prhs[3]));
unsigned short total_names_length = 0;
for(unsigned short i = 0; i < 3; i++)
total_names_length += mxGetN(mxGetCell(prhs[1], i));
char *var_names_storage = (char *)malloc(3 + total_names_length);
char *var_names[3];
var_names[0] = var_names_storage;
var_names[1] = var_names[0] + 1 + mxGetN(mxGetCell(prhs[1], 0));
var_names[2] = var_names[1] + 1 + mxGetN(mxGetCell(prhs[1], 1));
for(unsigned short i = 0; i < 3; i++) {
mxArray *the_var_name = mxGetCell(prhs[1], i);
mxGetString(the_var_name, var_names[i], 1 + mxGetN(the_var_name));
}
mxLogical *options = mxGetLogicals(prhs[2]);
debug_msg(2, "opening: %s\n", filename);
dta_file = fopen(filename, "rb");
if(!dta_file)
mexErrMsgTxt("Error opening file.");
// allocate on the heap so that memory debugging libraries that don't perform bounds checking
// for stack based allocations will work.
setup_control *setup_c = (setup_control *)malloc(sizeof(setup_control));
mx_m1_control *m1_c = (mx_m1_control *)malloc(sizeof(mx_m1_control));
mx_m2_control *m2_c = (mx_m2_control *)malloc(sizeof(mx_m2_control));
mx_m173_control *m173_c = (mx_m173_control *)malloc(sizeof(mx_m173_control));
mx_m211_control *m211_c = (mx_m211_control *)malloc(sizeof(mx_m211_control));
m110_data *p_info = (m110_data *)malloc(sizeof(m110_data));
memset(setup_c, 0, sizeof(setup_control));
memset(m1_c, 0, sizeof(mx_m1_control));
memset(m2_c, 0, sizeof(mx_m2_control));
memset(m173_c, 0, sizeof(mx_m173_control));
memset(m211_c, 0, sizeof(mx_m211_control));
memset(p_info, 0, sizeof(m110_data));
int n_pp_segs = 0;
setup_c->m1_c = m1_c;
setup_c->m2_c = m2_c;
setup_c->m173_c = m173_c;
setup_c->m211_c = m211_c;
setup_c->input_file_handle = dta_file;
setup_c->options = options;
m1_c->partial_power_segs_p = m2_c->partial_power_segs_p = &n_pp_segs;
m173_c->n_hitbased = m1_c->n_hitbased;
m1_c->has_waveforms = &m173_c->has_waveforms;
m1_c->process_waveforms = (bool)options[2];
m1_c->last_waveform_tot = m173_c->last_tot;
m173_c->last_hit_tot = m1_c->last_tot;
for(int i=0; i < (__AE_NUM_CHANNELS + 1); i++) {
m173_c->last_tot[i] = -1.0;
m1_c->last_tot[i] = -1.0;
}
m1_c->parametric_info = p_info;
memset(mx_ctx, NULL, sizeof(mx_ctx));
mx_ctx[1] = m1_c;
mx_ctx[2] = m2_c;
mx_ctx[5] = m1_c;
mx_ctx[6] = m2_c;
mx_ctx[8] = dta_file;
mx_ctx[23] = m173_c;
mx_ctx[24] = m173_c;
mx_ctx[26] = m173_c;
mx_ctx[42] = dta_file;
mx_ctx[109] = &n_pp_segs;
mx_ctx[106] = setup_c;
mx_ctx[110] = m1_c;
mx_ctx[128] = setup_c;
mx_ctx[173] = m173_c;
mx_ctx[211] = m211_c;
mx_setup_handlers_init(options[0], options[1], options[2], options[3]);
parse_dta_file(mx_handlers, mx_ctx, dta_file);
ret = setup(setup_c);
if(ret != 0) {
debug_msg(CRITICAL_MSG, "Setup was not successful\n");
goto done;
}
rewind(dta_file);
debug_msg(2, "setup complete...\n");
mx_handlers_init(options[0], options[1], options[2], options[3]);
parse_dta_file(mx_handlers, mx_ctx, dta_file);
debug_msg(2, "parsing complete...\n");
if(options[0])
mexPutVariable(ws, var_names[0], m1_c->matlab_array_handle);
if(options[1])
mexPutVariable(ws, var_names[1], m2_c->matlab_array_handle);
if(options[3])
mexPutVariable(ws, var_names[2], m211_c->matlab_array_handle);
debug_msg(2, "done...\n");
done:
if(m1_c->characteristics)
free(m1_c->characteristics);
if(m2_c->characteristics)
free(m2_c->characteristics);
if(m2_c->parametrics)
free(m2_c->parametrics);
if(p_info->pids)
free(p_info->pids);
free(setup_c);
free(m1_c);
free(m2_c);
free(m173_c);
free(m211_c);
free(p_info);
}
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
PVs pvs = { {0} };
int i,j,ij,n;
LcaError theErr;
MultiArgRec args[1];
enum_states *strbuf MAY_ALIAS = 0;
mxArray *tmp;
lcaErrorInit(&theErr);
LHSCHECK(nlhs, plhs);
if ( nlhs > 1 ) {
lcaSetError(&theErr, EZCA_INVALIDARG, "Too many output args");
goto cleanup;
}
if ( nrhs < 1 || nrhs > 1 ) {
lcaSetError(&theErr, EZCA_INVALIDARG, "Expected 1 rhs argument");
goto cleanup;
}
if ( buildPVs(prhs[0], &pvs, &theErr) )
goto cleanup;
MSetArg(args[0], sizeof(*strbuf), 0, &strbuf);
if ( !multi_ezca_get_misc(pvs.names, pvs.m, (MultiEzcaFunc)ezcaGetEnumStrings, NumberOf(args), args, &theErr) )
goto cleanup;
n = EZCA_ENUM_STATES;
/* convert string array to a matlab cell array of matlab strings */
if ( !(plhs[0] = mxCreateCellMatrix(pvs.m, n)) ) {
lcaSetError(&theErr, EZCA_FAILEDMALLOC, "Not enough memory");
goto cleanup;
}
ij = 0;
for ( j = 0; j < n; j++ ) {
for ( i = 0; i < pvs.m; i++ ) {
if ( !(tmp = mxCreateString(strbuf[i][j])) ) {
for ( j=0; j<ij; j++ ) {
mxDestroyArray(mxGetCell(plhs[0],ij));
}
mxDestroyArray(plhs[0]);
plhs[0] = 0;
lcaSetError(&theErr, EZCA_FAILEDMALLOC, "Not enough memory");
goto cleanup;
}
mxSetCell(plhs[0], ij, (mxArray*)tmp);
ij++;
}
}
nlhs = 0;
cleanup:
if ( strbuf )
lcaFree( strbuf );
releasePVs(&pvs);
/* do this LAST (in case mexErrMsgTxt is called) */
ERR_CHECK(nlhs, plhs, &theErr);
}
void
mexFunction (int nout, mxArray ** out, int nin, mxArray const ** in)
{
SAMPLE sample; /* training sample */
LEARN_PARM learn_parm;
KERNEL_PARM kernel_parm;
STRUCT_LEARN_PARM struct_parm;
STRUCTMODEL structmodel;
int alg_type;
enum {IN_ARGS=0, IN_SPARM} ;
enum {OUT_W=0} ;
/* SVM-light is not fully reentrant, so we need to run this patch first */
init_qp_solver() ;
verbosity = 0 ;
kernel_cache_statistic = 0 ;
if (nin != 2) {
mexErrMsgTxt("Two arguments required") ;
}
/* Parse ARGS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */
char arg [1024 + 1] ;
int argc ;
char ** argv ;
if (! uIsString(in[IN_ARGS], -1)) {
mexErrMsgTxt("ARGS must be a string") ;
}
mxGetString(in[IN_ARGS], arg, sizeof(arg) / sizeof(char)) ;
arg_split (arg, &argc, &argv) ;
svm_struct_learn_api_init(argc+1, argv-1) ;
read_input_parameters (argc+1,argv-1,
&verbosity, &struct_verbosity,
&struct_parm, &learn_parm,
&kernel_parm, &alg_type ) ;
if (kernel_parm.kernel_type != LINEAR &&
kernel_parm.kernel_type != CUSTOM) {
mexErrMsgTxt ("Only LINEAR or CUSTOM kerneles are supported") ;
}
/* Parse SPARM ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */
mxArray const * sparm_array = in [IN_SPARM] ;
mxArray const * patterns_array ;
mxArray const * labels_array ;
mxArray const * kernelFn_array ;
int numExamples, ei ;
if (! sparm_array) {
mexErrMsgTxt("SPARM must be a structure") ;
}
struct_parm.mex = sparm_array ;
patterns_array = mxGetField(sparm_array, 0, "patterns") ;
if (! patterns_array ||
! mxIsCell(patterns_array)) {
mexErrMsgTxt("SPARM.PATTERNS must be a cell array") ;
}
numExamples = mxGetNumberOfElements(patterns_array) ;
labels_array = mxGetField(sparm_array, 0, "labels") ;
if (! labels_array ||
! mxIsCell(labels_array) ||
! mxGetNumberOfElements(labels_array) == numExamples) {
mexErrMsgTxt("SPARM.LABELS must be a cell array "
"with the same number of elements of "
"SPARM.PATTERNS") ;
}
sample.n = numExamples ;
sample.examples = (EXAMPLE *) my_malloc (sizeof(EXAMPLE) * numExamples) ;
for (ei = 0 ; ei < numExamples ; ++ ei) {
sample.examples[ei].x.mex = mxGetCell(patterns_array, ei) ;
sample.examples[ei].y.mex = mxGetCell(labels_array, ei) ;
sample.examples[ei].y.isOwner = 0 ;
}
if (struct_verbosity >= 1) {
mexPrintf("There are %d training examples\n", numExamples) ;
}
kernelFn_array = mxGetField(sparm_array, 0, "kernelFn") ;
if (! kernelFn_array && kernel_parm.kernel_type == CUSTOM) {
mexErrMsgTxt("SPARM.KERNELFN must be define for CUSTOM kernels") ;
}
if (kernelFn_array) {
MexKernelInfo * info ;
if (mxGetClassID(kernelFn_array) != mxFUNCTION_CLASS) {
mexErrMsgTxt("SPARM.KERNELFN must be a valid function handle") ;
}
info = (MexKernelInfo*) kernel_parm.custom ;
info -> structParm = sparm_array ;
info -> kernelFn = kernelFn_array ;
}
/* Learning ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */
switch (alg_type) {
case 0:
svm_learn_struct(sample,&struct_parm,&learn_parm,&kernel_parm,&structmodel,NSLACK_ALG) ;
break ;
case 1:
svm_learn_struct(sample,&struct_parm,&learn_parm,&kernel_parm,&structmodel,NSLACK_SHRINK_ALG);
break ;
case 2:
svm_learn_struct_joint(sample,&struct_parm,&learn_parm,&kernel_parm,&structmodel,ONESLACK_PRIMAL_ALG);
break ;
case 3:
svm_learn_struct_joint(sample,&struct_parm,&learn_parm,&kernel_parm,&structmodel,ONESLACK_DUAL_ALG);
break ;
case 4:
svm_learn_struct_joint(sample,&struct_parm,&learn_parm,&kernel_parm,&structmodel,ONESLACK_DUAL_CACHE_ALG);
break ;
case 9:
svm_learn_struct_joint_custom(sample,&struct_parm,&learn_parm,&kernel_parm,&structmodel);
break ;
default:
mexErrMsgTxt("Unknown algorithm type") ;
}
/* Write output ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */
/* Warning: The model contains references to the original data 'docs'.
If you want to free the original data, and only keep the model, you
have to make a deep copy of 'model'. */
mxArray * model_array = newMxArrayEncapsulatingSmodel (&structmodel) ;
out[OUT_W] = mxDuplicateArray (model_array) ;
destroyMxArrayEncapsulatingSmodel (model_array) ;
free_struct_sample (sample) ;
free_struct_model (structmodel) ;
svm_struct_learn_api_exit () ;
free_qp_solver () ;
}
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) { ALLOCATES();
real *X, XX[NN], Xk[NN], XXr[NN], D[N], DS[N], fD[N], V[NN], VS[NN], *O, Ok[NN];
long k1, K1, k2, K2, k3, K3, ii, jj;
int ORDER[N];
char STR[100];
enum symmetrize_ { NONE , X_Xt , Xt_X , PLUS };
enum symmetrize_ symmetrize;
enum outs_types { ID , INVERSE , EIGVALS , EIGVECS , EIGVALSDIAG , MAXDIFF , SQRT , LOG , EXP , evalFUN , DET , TRACE };
enum outs_types outs[50];
int ndims, Odims[50];
real det;
int oid;
int D_computed, V_computed, D_sorted, V_sorted, ORDER_computed;
int dim1 , dim2;
mxArray *mxX;
if( nlhs == 0 ){ nlhs = 1; }
if( nlhs > nrhs-2 ){
myErrMsgTxt("There are no enough inputs.\n");
}
if( mxIsCell( prhs[0] ) ){
mxX = mxGetCell( prhs[0] , 0 );
dim1 = myGetValue( mxGetCell( prhs[0] , 1 ) );
dim2 = myGetValue( mxGetCell( prhs[0] , 2 ) );
} else {
mxX = prhs[0];
dim1 = 1;
dim2 = 2;
}
if( ( mySize( mxX , dim1-1 ) != N ) || ( mySize( mxX , dim1-1 ) != N ) ){
myErrMsgTxt("size( X , %d ) and size( X , %d ) have to be equal to three.\n",dim1,dim2);
}
if( myIsEmpty( prhs[1] ) ){
symmetrize = NONE;
} else if( mxIsChar(prhs[1]) ){
mxGetString( prhs[1], STR, 100 );
if( !myStrcmpi(STR,"+") ) {
symmetrize = PLUS;
} else if( !myStrcmpi(STR,"xt*x") || !myStrcmpi(STR,"xtx") ) {
symmetrize = Xt_X;
} else if( !myStrcmpi(STR,"x*xt") || !myStrcmpi(STR,"xxt") ) {
symmetrize = X_Xt;
} else {
myErrMsgTxt("Second argument expected: 'xt*x' , 'x*xt' , '+' , or [].\n");
}
} else {
myErrMsgTxt("Second argument expected: 'xt*x' , 'x*xt' , '+' , or [].\n");
}
for( oid = 0 ; oid < nlhs ; oid++ ){
if( ! mxIsChar(prhs[oid+2]) ){
myErrMsgTxt("Valids arguments are: 'id' 'eigval' 'eigvec' 'log' 'sqrt' 'exp' 'error'.\n");
}
mxGetString( prhs[oid+2], STR, 100 );
if( !myStrcmpi(STR,"id") ) {
outs[oid] = ID;
} else if( !myStrcmpi(STR,"inv") || !myStrcmpi(STR,"inverse") ) {
outs[oid] = INVERSE;
} else if( !myStrcmpi(STR,"det") ) {
outs[oid] = DET;
} else if( !myStrcmpi(STR,"trace") ) {
outs[oid] = TRACE;
} else if( !myStrcmpi(STR,"evec") || !myStrcmpi(STR,"v") || !myStrcmpi(STR,"eigenvec") || !myStrcmpi(STR,"eigvec") || !myStrcmpi(STR,"eigenvectors") ) {
outs[oid] = EIGVECS;
} else if( !myStrcmpi(STR,"eval") || !myStrcmpi(STR,"d") || !myStrcmpi(STR,"eigenval") || !myStrcmpi(STR,"eigval") || !myStrcmpi(STR,"eigenvalues") ) {
outs[oid] = EIGVALS;
} else if( !myStrcmpi(STR,"diag") || !myStrcmpi(STR,"dd") ) {
outs[oid] = EIGVALSDIAG;
} else if( !myStrcmpi(STR,"error") ) {
outs[oid] = MAXDIFF;
} else if( !myStrcmpi(STR,"sqrt") || !myStrcmpi(STR,"sqrtm") ) {
outs[oid] = SQRT;
} else if( !myStrcmpi(STR,"log") || !myStrcmpi(STR,"logm") ) {
outs[oid] = LOG;
} else if( !myStrcmpi(STR,"exp") || !myStrcmpi(STR,"expm") ) {
outs[oid] = EXP;
} else {
myErrMsgTxt("Valids arguments are: 'id' 'inv' 'det' 'trace' 'eigval' 'eigvec' 'log' 'sqrt' 'exp' 'error'.\n");
}
}
X = mxGetPr( mxX );
ndims = myGetSizes( mxX , Odims );
for( oid = 0 ; oid < nlhs ; oid++ ){
switch( outs[oid] ){
case ID:
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
break;
case INVERSE:
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
break;
case DET:
Odims[dim1-1] = 1;
Odims[dim2-1] = 1;
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
Odims[dim1-1] = N;
Odims[dim2-1] = N;
break;
case TRACE:
Odims[dim1-1] = 1;
Odims[dim2-1] = 1;
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
Odims[dim1-1] = N;
Odims[dim2-1] = N;
break;
case EIGVALS:
Odims[dim2-1] = 1;
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
Odims[dim2-1] = N;
break;
case EIGVECS:
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
break;
case EIGVALSDIAG:
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
break;
case MAXDIFF:
Odims[dim1-1] = 1;
Odims[dim2-1] = 1;
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
Odims[dim1-1] = N;
Odims[dim2-1] = N;
break;
case EXP:
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
break;
case LOG:
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
break;
case SQRT:
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
break;
case evalFUN:
plhs[oid] = mxCreateNumericArray( ndims , Odims , mxREAL_CLASS , mxREAL );
break;
}
}
K1 = 1;
for( k1 = 0 ; k1 < dim1-1 ; k1++ ){ K1 *= Odims[k1]; }
K2 = 1;
for( k2 = dim1 ; k2 < dim2-1 ; k2++ ){ K2 *= Odims[k2]; }
K3 = 1;
for( k3 = dim2 ; k3 < ndims ; k3++ ){ K3 *= Odims[k3]; }
for( k3 = 0 ; k3 < K3 ; k3++ ){
for( k2 = 0 ; k2 < K2 ; k2++ ){
for( k1 = 0 ; k1 < K1 ; k1++ ){
if( K1 == 1 && K2 == 1 ){
memcpy( Xk , X + k3*NN , NN*sizeof( real ) );
} else {
for( jj = 0 ; jj < N ; jj++ ){ for( ii = 0 ; ii < N ; ii++ ){
Xk[ ii + N*jj ] = X[ k1 + K1*( ii + N*( k2 + K2*( jj + N*k3 ))) ];
} }
}
switch( symmetrize ){
case NONE:
memcpy( XX , Xk , NN*sizeof( real ) );
break;
case X_Xt:
XX[0] = Xk[0]*Xk[0] + Xk[2]*Xk[2];
XX[1] = Xk[1]*Xk[0] + Xk[3]*Xk[2];
XX[2] = Xk[0]*Xk[1] + Xk[2]*Xk[3];
XX[3] = Xk[1]*Xk[1] + Xk[3]*Xk[3];
break;
case Xt_X:
XX[0] = Xk[0]*Xk[0] + Xk[1]*Xk[1];
XX[1] = Xk[2]*Xk[0] + Xk[3]*Xk[1];
XX[2] = Xk[0]*Xk[2] + Xk[1]*Xk[3];
XX[3] = Xk[2]*Xk[2] + Xk[3]*Xk[3];
break;
case PLUS:
XX[0] = Xk[0];
XX[1] = XX[2] = ( Xk[1] + Xk[2] )/2.0;
XX[3] = Xk[3];
break;
}
D_computed = 0;
V_computed = 0;
ORDER_computed = 0;
D_sorted = 0;
V_sorted = 0;
for( oid = 0 ; oid < nlhs ; oid++ ){
switch( outs[oid] ){
case ID:
memcpy( Ok , XX , NN*sizeof( real ) );
O = mxGetPr( plhs[oid] );
ToOutput2x2;
break;
case INVERSE:
det = XX[0]*XX[3] - XX[1]*XX[2];
det = 1.0/det;
Ok[0] = XX[3] *det;
Ok[1] = -XX[1] *det;
Ok[2] = -XX[2] *det;
Ok[3] = XX[0] *det;
O = mxGetPr( plhs[oid] );
ToOutput2x2;
break;
case DET:
Ok[0] = XX[0]*XX[3] - XX[1]*XX[2];
O = mxGetPr( plhs[oid] );
ToOutput1x1;
break;
case TRACE:
Ok[0] = XX[0] + XX[3];
O = mxGetPr( plhs[oid] );
ToOutput1x1;
break;
case EIGVALS:
if( !D_computed ){ EigenValues2x2( XX , D ); D_computed = 1; }
if( !ORDER_computed ){ GetOrder( D, ORDER ); ORDER_computed = 1; }
if( !D_sorted ){ SortEigenValues( D, ORDER , DS ); D_sorted = 1; }
memcpy( Ok , DS , N*sizeof( real ) );
O = mxGetPr( plhs[oid] );
ToOutput2x1;
break;
case EIGVALSDIAG:
if( !D_computed ){ EigenValues2x2( XX , D ); D_computed = 1; }
if( !ORDER_computed ){ GetOrder( D, ORDER ); ORDER_computed = 1; }
if( !D_sorted ){ SortEigenValues( D, ORDER , DS ); D_sorted = 1; }
Ok[0] = DS[0];
Ok[3] = DS[1];
Ok[1] = Ok[2] = 0;
O = mxGetPr( plhs[oid] );
ToOutput2x2;
break;
case EIGVECS:
if( !D_computed ){ EigenValues2x2( XX , D ); D_computed = 1; }
if( !V_computed ){ EigenVectors2x2( XX , D , V); V_computed = 1; }
if( !ORDER_computed ){ GetOrder( D, ORDER ); ORDER_computed = 1; }
if( !V_sorted ){ SortEigenVectors( V, ORDER , VS); V_sorted = 1; }
memcpy( Ok , VS , NN*sizeof( real ) );
O = mxGetPr( plhs[oid] );
ToOutput2x2;
break;
// case MAXDIFF:
// if( !D_computed ){ EigenValuesSym3x3( XX , D ); D_computed = 1; }
// if( !V_computed ){ EigenVectorsSym3x3( XX , D , V); V_computed = 1; }
//
// Ok[0] = V[0]*V[0]*D[0] + V[3]*V[3]*D[1] + V[6]*V[6]*D[2];
// Ok[1] = V[1]*V[0]*D[0] + V[4]*V[3]*D[1] + V[7]*V[6]*D[2];
// Ok[2] = V[2]*V[0]*D[0] + V[5]*V[3]*D[1] + V[8]*V[6]*D[2];
//
// Ok[3] = V[0]*V[1]*D[0] + V[3]*V[4]*D[1] + V[6]*V[7]*D[2];
// Ok[4] = V[1]*V[1]*D[0] + V[4]*V[4]*D[1] + V[7]*V[7]*D[2];
// Ok[5] = V[2]*V[1]*D[0] + V[5]*V[4]*D[1] + V[8]*V[7]*D[2];
//
// Ok[6] = V[0]*V[2]*D[0] + V[3]*V[5]*D[1] + V[6]*V[8]*D[2];
// Ok[7] = V[1]*V[2]*D[0] + V[4]*V[5]*D[1] + V[7]*V[8]*D[2];
// Ok[8] = V[2]*V[2]*D[0] + V[5]*V[5]*D[1] + V[8]*V[8]*D[2];
//
// Ok[0] = MAX9( fabs( Ok[0] - XX[0] ) ,
// fabs( Ok[1] - XX[1] ) ,
// fabs( Ok[2] - XX[2] ) ,
// fabs( Ok[3] - XX[3] ) ,
// fabs( Ok[4] - XX[4] ) ,
// fabs( Ok[5] - XX[5] ) ,
// fabs( Ok[6] - XX[6] ) ,
// fabs( Ok[7] - XX[7] ) ,
// fabs( Ok[8] - XX[8] ) );
//
// O = mxGetPr( plhs[oid] );
// ToOutput1x1;
// break;
//
//
// case SQRT:
// if( !D_computed ){ EigenValuesSym3x3( XX , D ); D_computed = 1; }
// if( !V_computed ){ EigenVectorsSym3x3( XX , D , V); V_computed = 1; }
//
// fD[0] = sqrt( D[0] );
// fD[1] = sqrt( D[1] );
// fD[2] = sqrt( D[2] );
//
// FillOk;
// O = mxGetPr( plhs[oid] );
// ToOutput3x3;
// break;
//
//
// case LOG:
// if( !D_computed ){ EigenValuesSym3x3( XX , D ); D_computed = 1; }
// if( !V_computed ){ EigenVectorsSym3x3( XX , D , V); V_computed = 1; }
//
// fD[0] = log( D[0] );
// fD[1] = log( D[1] );
// fD[2] = log( D[2] );
//
// FillOk;
// O = mxGetPr( plhs[oid] );
// ToOutput3x3;
// break;
#define r eval[0]
#define e eval[1]
#define er eval[2]
case EXP:
r = XX[0] - XX[3];
r = 4*XX[1]*XX[2] + r*r;
if( r >= 0 ){
r = sqrt(r);
e = exp( ( XX[0] + XX[3] - r )/2 )/r/2.0;
er = exp(r);
Ok[0] = e * ( XX[3] - XX[0] + r + er*(XX[0]-XX[3]+r) );
Ok[1] = e * XX[1] * ( er - 1 ) * 2;
Ok[2] = e * XX[2] * ( er - 1 ) * 2;
Ok[3] = e * ( XX[0] - XX[3] + r + er*(XX[3]-XX[0]+r) );
} else {
r = sqrt( -r );
e = exp( ( XX[0] + XX[3] )/2 )/r;
er = sin(r/2);
Ok[0] = e * ( r*cos(r/2) + ( XX[0]-XX[3] )*er );
Ok[1] = 2 * XX[1] * e * er;
Ok[2] = 2 * XX[2] * e * er;
Ok[3] = e * ( r*cos(r/2) + ( XX[3]-XX[0] )*er );
}
O = mxGetPr( plhs[oid] );
ToOutput2x2;
break;
// case evalFUN:
// O = mxGetPr( plhs[oid] ) + k*NN;
// if( !D_computed ){ EigenValuesSym3x3( XX , D ); D_computed = 1; }
// if( !V_computed ){ EigenVectorsSym3x3( XX , D , V); V_computed = 1; }
//
// fD[0] = exp( D[0] );
// fD[1] = exp( D[1] );
// fD[2] = exp( D[2] );
//
// mexCallMATLAB(int nlhs, mxArray *plhs[], int nrhs, mxArray *prhs[], const char *name)
//
// FillO
// break;
}
}
}}}
EXIT: myFreeALLOCATES();
}
void mexFunction (int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
mwSize n;
float *b , *x;
ldl_p chol;
mwSize i;
mwIndex *jld;
s_hlevel *H;
int nlevels;
mxArray *C;
/* Input validation */
if (nrhs !=2)
mexErrMsgTxt("Wrong number of input arguments");
if (!mxIsCell(H_IN))
mexErrMsgTxt("First argument must be a Hierarchy cell");
if (!mxIsSingle(b_IN))
mexErrMsgTxt("Second argument must be a non-sparse single precision vector");
if ( (mxGetN(b_IN)!=1))
mexErrMsgTxt("Second argument must be a column vector");
n = mxGetM(b_IN);
nlevels = (int) MAX(mxGetM(H_IN),mxGetN(H_IN));
H = malloc(nlevels*sizeof(s_hlevel));
if (nlevels>1) {
C = mxGetCell(H_IN,nlevels-2);
H[nlevels-2].islast = (boolean) *(mxGetPr(mxGetField(C,0,"islast")));
if (H[nlevels-2].islast)
nlevels = nlevels-1;
}
for (i=0; i<nlevels; i++) {
C = mxGetCell(H_IN,i);
H[i].islast = (boolean) *(mxGetPr(mxGetField(C,0,"islast")));
H[i].iterative = (boolean) *(mxGetPr(mxGetField(C,0,"iterative")));
if (i<(nlevels-1)) {
H[i].cI = (mIndex *) mxGetPr(mxGetField(C,0,"cI"));
H[i].nc = (mSize) *(mxGetPr(mxGetField(C,0,"nc")));
H[i].invD = (float *) mxGetPr(mxGetField(C,0,"invD"));
H[i].dc = (boolean) *(mxGetPr(mxGetField(C,0,"dc")));
H[i].repeat = (int) *(mxGetPr(mxGetField(C,0,"repeat")));
H[i].lws1 = (float *) mxGetPr(mxGetField(C,0,"lws1"));
H[i].lws2 = (float *) mxGetPr(mxGetField(C,0,"lws2"));
H[i].sws1 = (float *) mxGetPr(mxGetField(C,0,"sws1"));
H[i].sws2 = (float *) mxGetPr(mxGetField(C,0,"sws2"));
H[i].sws3 = (float *) mxGetPr(mxGetField(C,0,"sws3"));
}
if (i==0)
H[i].laplacian = (boolean) *(mxGetPr(mxGetField(C,0,"laplacian")));
H[i].A.a = (float *) mxGetPr(mxGetField(mxGetField(C,0,"A"),0,"a"));
H[i].A.ia = (mIndex *) mxGetPr(mxGetField(mxGetField(C,0,"A"),0,"ia"));
H[i].A.ja = (mIndex *) mxGetPr(mxGetField(mxGetField(C,0,"A"),0,"ja"));
H[i].A.n = (mSize) *(mxGetPr(mxGetField(mxGetField(C,0,"A"),0,"n")));
H[i].A.issym = (boolean) *(mxGetPr(mxGetField(mxGetField(C,0,"A"),0,"issym")));
if (i==(nlevels-1)){
if (!H[i].iterative){
H[i].chol.ld.a = (double *) mxGetPr(mxGetField(mxGetField(mxGetField(C,0,"chol"),0,"ld"),0,"a"));
H[i].chol.ld.ia = (mIndex *) mxGetPr(mxGetField(mxGetField(mxGetField(C,0,"chol"),0,"ld"),0,"ia"));
H[i].chol.ld.ja = (mIndex *) mxGetPr(mxGetField(mxGetField(mxGetField(C,0,"chol"),0,"ld"),0,"ja"));
H[i].chol.ld.n = (mSize ) *(mxGetPr(mxGetField(mxGetField(mxGetField(C,0,"chol"),0,"ld"),0,"n")));
H[i].chol.ldT.a = (double *) mxGetPr(mxGetField(mxGetField(mxGetField(C,0,"chol"),0,"ldT"),0,"a"));
H[i].chol.ldT.ia = (mIndex *) mxGetPr(mxGetField(mxGetField(mxGetField(C,0,"chol"),0,"ldT"),0,"ia"));
H[i].chol.ldT.ja = (mIndex *) mxGetPr(mxGetField(mxGetField(mxGetField(C,0,"chol"),0,"ldT"),0,"ja"));
H[i].chol.ldT.n = (mSize ) *(mxGetPr(mxGetField(mxGetField(mxGetField(C,0,"chol"),0,"ldT"),0,"n")));
H[i].chol.p = (mIndex *) mxGetPr(mxGetField(mxGetField(C,0,"chol"),0,"p"));
H[i].chol.invp = (mIndex *) mxGetPr(mxGetField(mxGetField(C,0,"chol"),0,"invp"));
}
else {
H[i].invD = (float *) mxGetPr(mxGetField(C,0,"invD"));
H[i].lws1 = (float *) mxGetPr(mxGetField(C,0,"lws1"));
H[i].lws2 = (float *) mxGetPr(mxGetField(C,0,"lws2"));
H[i].sws1 = (float *) mxGetPr(mxGetField(C,0,"sws1"));
H[i].sws2 = (float *) mxGetPr(mxGetField(C,0,"sws2"));
H[i].sws3 = (float *) mxGetPr(mxGetField(C,0,"sws3"));
}
}
}
b = (float *) mxGetPr(b_IN);
x_OUT = mxCreateNumericArray(1,&n,mxSINGLE_CLASS,mxREAL);
x = (float *) mxGetPr(x_OUT);
preconditioner( H, b, 0, 1,x);
free(H);
return;
}
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
int dim, m, n, l, ntot, dims[3];
float *data1, *data2, *data20, *data21, *data22, *data23,*wx, *wy, *wz;
double spline, nx, ny, nz, offx, offy, offz, mx, my, mz;
size_t sizebuf;
if (nrhs == 6)
{
spline = mxGetScalar(prhs[5]);
}
else if (nrhs == 5)
{
spline = 3;
}
else
{
mexPrintf("[Gxx Gyx Gzx Gxy Gyy Gzy Gxz Gyz Gzz] = "
"BsplCos2ValsMaskZero(COEFFx, COEFFy, COEFFz, "
"[nx ny nz], [offx offy offz], [mx my mz], MASK, deg);\n");
mexPrintf("[in]\n");
mexPrintf("\tCOEFFx COEFFy COEFFz: bspline coefficients - "
"single type\n");
mexPrintf("\t[nx ny nz] : output dimension\n");
mexPrintf("\t[offx offy offz] : offset of the origin\n");
mexPrintf("\t[mx my mz] : magnification factor for "
"each direction\n");
mexPrintf("\tMASK : MASK, non zeros");
mexPrintf("\tdeg : (opt) spline basis degree "
"{default: 3}\n");
mexPrintf("[out]\n");
mexPrintf("\tGx Gy Gz, x y z : gradient values\n");
return;
}
if (mxIsSingle(prhs[0]) != 1)
{
mexErrMsgTxt("First argument must be of single type\n");
return;
}
/* Retrieve the input data */
data1 = mxGetData(prhs[0]);
if (mxGetNumberOfDimensions(prhs[0]) == 2)
{
m = mxGetDimensions(prhs[0])[0];
n = mxGetDimensions(prhs[0])[1];
l = 1;
}
else if (mxGetNumberOfDimensions(prhs[0]) == 3)
{
m = mxGetDimensions(prhs[0])[0];
n = mxGetDimensions(prhs[0])[1];
l = mxGetDimensions(prhs[0])[2];
}
else
{
mexErrMsgTxt("First argument must be 2D or 3D\n");
return;
}
ntot = mxGetNumberOfElements(prhs[1]);
dim = ntot;
sizebuf = mxGetElementSize(prhs[1]);
if (ntot == 2)
{
nx = *((double*)mxGetData(prhs[1]));
ny = *((double*)(mxGetData(prhs[1]) + sizebuf));
dims[0] = (int)nx;
dims[1] = (int)ny;
}
else if (ntot == 3)
{
nx = *((double*)mxGetData(prhs[1]));
ny = *((double*)(mxGetData(prhs[1]) + sizebuf));
nz = *((double*)(mxGetData(prhs[1]) + 2*sizebuf));
dims[0] = (int)nx;
dims[1] = (int)ny;
dims[2] = (int)nz;
}
else
{
mexErrMsgTxt("Second argument should be either [nx ny nz] or "
"[nx ny]\n");
return;
}
ntot = mxGetNumberOfElements(prhs[2]);
sizebuf = mxGetElementSize(prhs[2]);
if (ntot == 2)
{
offx = *((double*)mxGetData(prhs[2]));
offy = *((double*)(mxGetData(prhs[2]) + sizebuf));
}
else if (ntot == 3)
{
offx = *((double*)mxGetData(prhs[2]));
offy = *((double*)(mxGetData(prhs[2]) + sizebuf));
offz = *((double*)(mxGetData(prhs[2]) + 2*sizebuf));
}
else
{
mexErrMsgTxt("Third argument should be either [offx offy offz]"
" or [offx offy]\n");
return;
}
ntot = mxGetNumberOfElements(prhs[3]);
sizebuf = mxGetElementSize(prhs[3]);
if (ntot == 2)
{
mx = *((double*)mxGetData(prhs[3]));
my = *((double*)(mxGetData(prhs[3]) + sizebuf));
}
else if (ntot == 3)
{
mx = *((double*)mxGetData(prhs[3]));
my = *((double*)(mxGetData(prhs[3]) + sizebuf));
mz = *((double*)(mxGetData(prhs[3]) + 2*sizebuf));
}
else
{
mexErrMsgTxt("Fourth argument should be either [mx my mz] or"
" [mx my]\n");
return;
}
ntot = mxGetNumberOfElements(prhs[4]);
if (ntot == 0)
{
}
else if (ntot == 2)
{
wx = (float*)mxGetData(mxGetCell(prhs[4], 0));
wy = (float*)mxGetData(mxGetCell(prhs[4], 1));
}
else if (ntot == 3)
{
wx = (float*)mxGetData(mxGetCell(prhs[4], 0));
wy = (float*)mxGetData(mxGetCell(prhs[4], 1));
wz = (float*)mxGetData(mxGetCell(prhs[4], 2));
}
else
{
mexErrMsgTxt("Fifth argument should be {}, {wx wy wz} or "
"{wx wy}\n");
return;
}
/* Create an mxArray for the output data */
if (dim == 3)
{
if (nlhs == 4)
{
plhs[0] = mxCreateNumericArray(
mxGetNumberOfElements(prhs[1]), dims,
mxSINGLE_CLASS, mxREAL);
plhs[1] = mxCreateNumericArray(
mxGetNumberOfElements(prhs[1]), dims,
mxSINGLE_CLASS, mxREAL);
plhs[2] = mxCreateNumericArray(
mxGetNumberOfElements(prhs[1]), dims,
mxSINGLE_CLASS, mxREAL);
plhs[3] = mxCreateNumericArray(
mxGetNumberOfElements(prhs[1]), dims,
mxSINGLE_CLASS, mxREAL);
data20 = mxGetData(plhs[0]);
data21 = mxGetData(plhs[1]);
data22 = mxGetData(plhs[2]);
data23 = mxGetData(plhs[3]);
if (ntot == 0) /* no warp */
{
BatchInterpolatedAll3DZero (
data20, data21, data22, data23, data1,
m, n, l, nx, offx, mx, ny, offy, my,
nz, offz, mz, (long)spline);
}
else
{
BatchInterpolatedAll3DZeroWarp (
data20, data21, data22, data23, data1,
m, n, l, nx, offx, mx, wx, ny, offy, my,
wy, nz, offz, mz, wz, (long)spline);
}
}
else
{
plhs[0] = mxCreateNumericArray(
mxGetNumberOfElements(prhs[1]), dims,
mxSINGLE_CLASS, mxREAL);
data2 = mxGetData(plhs[0]);
if (ntot == 0) /* no warp */
{
BatchInterpolatedValue3DZero(data2, data1,
m, n, l, nx, offx, mx, ny, offy, my,
nz, offz, mz, (long)spline);
}
else
{
BatchInterpolatedValue3DZeroWarp(data2, data1,
m, n, l, nx, offx, mx, wx, ny, offy, my,
wy, nz, offz, mz, wz, (long)spline);
}
}
}
else
{
if (nlhs == 3)
{
plhs[0] = mxCreateNumericArray(
mxGetNumberOfElements(prhs[1]), dims,
mxSINGLE_CLASS, mxREAL);
plhs[1] = mxCreateNumericArray(
mxGetNumberOfElements(prhs[1]), dims,
mxSINGLE_CLASS, mxREAL);
plhs[2] = mxCreateNumericArray(
mxGetNumberOfElements(prhs[1]), dims,
mxSINGLE_CLASS, mxREAL);
data20 = mxGetData(plhs[0]);
data21 = mxGetData(plhs[1]);
data22 = mxGetData(plhs[2]);
if (ntot == 0) /* no warp */
{
BatchInterpolatedValue2DZero(data20,data1, m, n,
nx, offx, mx, ny, offy, my,
(long)spline);
BatchInterpolatedGradX2DZero(data21,data1, m, n,
nx, offx, mx, ny, offy, my,
(long)spline);
BatchInterpolatedGradY2DZero(data22,data1, m, n,
nx, offx, mx, ny, offy, my,
(long)spline);
}
else
{
BatchInterpolatedValue2DZeroWarp(data20, data1,
m, n, nx, offx, mx, wx, ny, offy, my,wy,
(long)spline);
BatchInterpolatedGradX2DZeroWarp(data21, data1,
m, n, nx, offx, mx, wx, ny, offy, my,wy,
(long)spline);
BatchInterpolatedGradY2DZeroWarp(data22, data1,
m, n, nx, offx, mx, wx, ny, offy, my,wy,
(long)spline);
}
}
else
{
plhs[0] = mxCreateNumericArray(
mxGetNumberOfElements(prhs[1]), dims,
mxSINGLE_CLASS, mxREAL);
data2 = mxGetData(plhs[0]);
if (ntot == 0) /* no warp */
{
BatchInterpolatedValue2DZero(data2, data1, m, n,
nx, offx, mx, ny, offy, my,
(long)spline);
}
else
{
BatchInterpolatedValue2DZeroWarp(data2, data1,
m, n, nx, offx, mx, wx, ny, offy, my,wy,
(long)spline);
}
}
}
}
// Create object from MATLAB struct variable.
// mx_shear is a struct containing the following fields:
// * fftPlanMany (array of forward FFT R2C plans, one multiplan per scale)
// * ifftPlanMany (array of inverse FFT C2R plans, one multiplan per scale)
// * fftPlanOne (one FFT R2C plan for a single image)
// * filter (cell array of filters, one cell element per scale)
bool ShearDictionary::loadFromMx(const mxArray* mx_shear, GPUmat* gm)
{
if( hasData() )
{
mexErrMsgTxt( "Method ShearDictionary::loadFromMx() should only be called once" );
return false;
}
// Get fields
mxArray* mx_filter = mxGetField( mx_shear, 0, "filter" );
mxArray* mx_fftPlanMany = mxGetField( mx_shear, 0, "fftPlanMany" );
mxArray* mx_ifftPlanMany = mxGetField( mx_shear, 0, "ifftPlanMany" );
mxArray* mx_fftPlanOne= mxGetField( mx_shear, 0, "fftPlanOne" );
// Check size of first element
mxArray* mx_filter_elem = mxGetCell(mx_filter, 0);
// Get attributes
GPUtype firstElem = gm->gputype.getGPUtype(mx_filter_elem);
m_type = gm->gputype.getType(firstElem);
if( m_type != gpuCFLOAT && m_type != gpuCDOUBLE )
{
mexErrMsgTxt("Filters should be complex of type GPUsingle or GPUdouble");
return false;
}
m_nFilterLen = gm->gputype.getSize(firstElem)[0];
// Check number of elements
int numScales = (int)mxGetNumberOfElements(mx_filter);
m_anNumDirections.resize(numScales);
m_GPUtypeData.resize(numScales);
// Check dimensions and get pointers
for (int j = 0; j < numScales; j++)
{
mx_filter_elem = mxGetCell(mx_filter, (mwIndex)j);
m_GPUtypeData[j] = gm->gputype.getGPUtype(mx_filter_elem);
// Check filter type
gpuTYPE_t type = gm->gputype.getType( m_GPUtypeData[j] );
if( type != m_type )
{
mexErrMsgTxt("Filters should be of GPUsingle or GPUdouble and type should be consistent");
return false;
}
// Check filter dimensions
int numDims = gm->gputype.getNdims(m_GPUtypeData[j]);
const int *dims = gm->gputype.getSize(m_GPUtypeData[j]);
if (numDims>2)
m_anNumDirections[j] = dims[2];
else
m_anNumDirections[j] = 1;
if (dims[1] != (m_nFilterLen/2+1) || dims[0] != m_nFilterLen ) {
mexErrMsgTxt("Filters should have same dimensions");
return false;
}
}
// Get pointers to FFT plans
m_fftPlanMany = (cufftHandle*)mxGetData( mx_fftPlanMany );
m_ifftPlanMany = (cufftHandle*)mxGetData( mx_ifftPlanMany );
m_fftPlanOne = *(cufftHandle*)mxGetData( mx_fftPlanOne );
// Set GPUmat environment
m_gm = gm;
return true;
}
/* read in input variables and run the algorithm */
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
int orient, img, i, j, c, x, y;
mxArray *f;
c = 0;
/* about active basis */
numOrient = ROUND(mxGetScalar(prhs[c++]));
locationShiftLimit = ROUND(mxGetScalar(prhs[c++]));
orientShiftLimit = ROUND(mxGetScalar(prhs[c++]));
subsample = ROUND(mxGetScalar(prhs[c++]));
numElement = ROUND(mxGetScalar(prhs[c++]));
/* about input images */
numImage = ROUND(mxGetScalar(prhs[c++]));
sizex = ROUND(mxGetScalar(prhs[c++]));
sizey = ROUND(mxGetScalar(prhs[c++]));
SUM1map = mxCalloc(numImage*numOrient, sizeof(float*));
for (img=0; img<numImage; img++)
for (orient=0; orient<numOrient; orient++)
{
i = orient*numImage+img;
f = mxGetCell(prhs[c], i);
SUM1map[i] = mxGetPr(f);
}
c++;
/* about Gabor filters */
halfFilterSize = ROUND(mxGetScalar(prhs[c++]));
Correlation = mxCalloc(numOrient*numOrient, sizeof(double*));
for (orient=0; orient<numOrient; orient++)
{
for (j=0; j<numOrient; j++)
{
f = mxGetCell(prhs[c], j*numOrient+orient);
Correlation[j*numOrient+orient] = mxGetPr(f);
}
}
c++;
allSymbol = mxCalloc(numOrient, sizeof(double*));
for (orient=0; orient<numOrient; orient++)
{
f = mxGetCell(prhs[c], orient);
allSymbol[orient] = mxGetPr(f);
}
c++;
/* about exponential model */
numStoredPoint = ROUND(mxGetScalar(prhs[c++]));
storedlambda = mxGetPr(prhs[c++]);
storedExpectation = mxGetPr(prhs[c++]);
storedLogZ = mxGetPr(prhs[c++]);
/* learned parameters of active basis */
selectedOrient = mxGetPr(prhs[c++]);
selectedx = mxGetPr(prhs[c++]);
selectedy = mxGetPr(prhs[c++]);
selectedlambda = mxGetPr(prhs[c++]);
selectedLogZ = mxGetPr(prhs[c++]);
/* templates of images */
commonTemplate = mxGetPr(prhs[c++]);
deformedTemplate = mxCalloc(numImage, sizeof(float*));
for (img=0; img<numImage; img++)
{
f = mxGetCell(prhs[c], img);
deformedTemplate[img] = mxGetPr(f);
}
c++;
for (x=1; x<=sizex; x++)
for (y=1; y<=sizey; y++)
commonTemplate[px(x, y, sizex, sizey)] = 0.;
for (img=0; img<numImage; img++)
{
for (x=1; x<=sizex; x++)
for (y=1; y<=sizey; y++)
deformedTemplate[img][px(x, y, sizex, sizey)] = 0.;
}
/* MAX1 maps are smaller than SUM1 maps */
sizexSubsample = floor((double)sizex/subsample);
sizeySubsample = floor((double)sizey/subsample);
/* run the shared sketch algorithm */
StoreShift();
InitializeMAX1map();
PursueElement();
/* free matrices to avoid memory leak */
free_matrix(pooledMax1map, numOrient, sizexSubsample*sizeySubsample);
free_matrix(MAX1map, numImage*numOrient, sizexSubsample*sizeySubsample);
free_matrix(trackMap, numImage*numOrient, sizexSubsample*sizeySubsample);
free_matrix(xShift, numOrient, numShift);
free_matrix(yShift, numOrient, numShift);
free_matrix(orientShifted, numOrient, numShift);
}
void mcaMonitorEventHandler(struct event_handler_args arg)
{ union db_access_val *pBuf;
struct mca_channel* PCHNL = (struct mca_channel*)arg.usr;
double *myDblPr;
chtype RequestType;
int i,Cnt;
mxArray* mymxArray;
pBuf = (union db_access_val *)arg.dbr;
//mexPrintf("MCA Monitor Event Handler Called\n");
PCHNL->MonitorEventCount++;
Cnt = ca_element_count(arg.chid);
RequestType = dbf_type_to_DBR(ca_field_type(arg.chid)); // Closest to the native
if(RequestType==DBR_STRING)
{ if(Cnt==1)
{ mxDestroyArray(PCHNL->CACHE); // clear mxArray that pointed to by PCHNL->CACHE
PCHNL->CACHE = mxCreateString((char*)((pBuf)->strval)); // Create new array with current string value
mexMakeArrayPersistent(PCHNL->CACHE);
}
else
{ for(i=0;i<Cnt;i++)
{ mymxArray = mxGetCell(PCHNL->CACHE,i);
mxDestroyArray(mymxArray);
mymxArray = mxCreateString( (char*) (&(pBuf->strval)+i) );
mexMakeArrayPersistent(mymxArray);
mxSetCell(PCHNL->CACHE,i,mymxArray);
}
}
}
else
{ myDblPr = mxGetPr(PCHNL->CACHE);
switch(RequestType)
{ case DBR_INT: // As defined in db_access.h DBR_INT = DBR_SHORT = 1
for (i = 0; i<Cnt;i++)
myDblPr[i]= (double)(*(&((pBuf)->intval)+i));
break;
case DBR_FLOAT:
for (i = 0; i<Cnt;i++)
myDblPr[i]= (double)(*(&((pBuf)->fltval)+i));
break;
case DBR_ENUM:
for (i = 0; i<Cnt;i++)
myDblPr[i]= (double)(*(&((pBuf)->enmval)+i));
break;
case DBR_CHAR:
for (i = 0; i<Cnt;i++)
myDblPr[i]= (double)(*(&((pBuf)->charval)+i));
break;
case DBR_LONG:
for (i = 0; i<Cnt;i++)
myDblPr[i]= (double)(*(&((pBuf)->longval)+i));
break;
case DBR_DOUBLE:
for (i = 0; i<Cnt;i++)
myDblPr[i]= (double)(*(&((pBuf)->doubleval)+i));
break;
}
}
if(PCHNL->MonitorCBString)
{
mexEvalString(PCHNL->MonitorCBString);
}
}
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[] )
{ mxArray *blk_cell_pr;
double *A, *B, *AI, *BI, *blksize;
mwIndex *irA, *jcA, *irB, *jcB;
int *cumblksize, *blknnz;
int mblk, isspA, isspB, iscmpA;
mwIndex subs[2];
mwSize nsubs=2;
int m, n, n2, nsub, k, index, numblk, NZmax, type;
double r2;
/* CHECK FOR PROPER NUMBER OF ARGUMENTS */
if (nrhs < 2){
mexErrMsgTxt("mexsvec: requires at least 2 input arguments."); }
if (nlhs > 1){
mexErrMsgTxt("mexsvec: requires 1 output argument."); }
/* CHECK THE DIMENSIONS */
mblk = mxGetM(prhs[0]);
if (mblk > 1) {
mexErrMsgTxt("mexsvec: blk can have only 1 row."); }
m = mxGetM(prhs[1]);
n = mxGetN(prhs[1]);
if (m != n) {
mexErrMsgTxt("mexsvec: matrix must be square."); }
subs[0] = 0; subs[1] = 1;
index = mxCalcSingleSubscript(prhs[0],nsubs,subs);
blk_cell_pr = mxGetCell(prhs[0],index);
numblk = mxGetN(blk_cell_pr);
blksize = mxGetPr(blk_cell_pr);
if (numblk == 1) {
n2 = n*(n+1)/2;
} else {
cumblksize = mxCalloc(numblk+1,sizeof(int));
blknnz = mxCalloc(numblk+1,sizeof(int));
cumblksize[0] = 0; blknnz[0] = 0;
n = 0; n2 = 0;
for (k=0; k<numblk; ++k) {
nsub = (int) blksize[k];
n += nsub;
n2 += nsub*(nsub+1)/2;
cumblksize[k+1] = n;
blknnz[k+1] = n2; }
}
/***** assign pointers *****/
A = mxGetPr(prhs[1]);
isspA = mxIsSparse(prhs[1]);
iscmpA = mxIsComplex(prhs[1]);
if (isspA) { irA = mxGetIr(prhs[1]);
jcA = mxGetJc(prhs[1]);
NZmax = mxGetNzmax(prhs[1]);
} else {
NZmax = n2;
}
if (iscmpA) { AI = mxGetPi(prhs[1]); }
if ((numblk > 1) & (!isspA)) {
mexErrMsgTxt("mexsvec: matrix must be sparse for numblk > 1"); }
if (nrhs > 2) {
if (mxGetM(prhs[2])>1) { isspB = (int)*mxGetPr(prhs[2]); }
else if (NZmax < n2/2) { isspB = 1; }
else { isspB = 0; }
} else {
if (NZmax < n2/2) { isspB = 1; }
else { isspB = 0; }
}
if (nrhs > 3) { type = (int)*mxGetPr(prhs[3]); }
else { type = 0; }
/***** create return argument *****/
if (isspB) {
if (iscmpA) {
plhs[0] = mxCreateSparse(n2,1,NZmax,mxCOMPLEX);
} else {
plhs[0] = mxCreateSparse(n2,1,NZmax,mxREAL);
}
B = mxGetPr(plhs[0]);
irB = mxGetIr(plhs[0]);
jcB = mxGetJc(plhs[0]);
jcB[0] = 0;
} else {
if (iscmpA) {
plhs[0] = mxCreateDoubleMatrix(n2,1,mxCOMPLEX);
} else {
plhs[0] = mxCreateDoubleMatrix(n2,1,mxREAL);
}
B = mxGetPr(plhs[0]);
}
if (iscmpA) { BI = mxGetPi(plhs[0]); }
/***** Do the computations in a subroutine *****/
r2 = sqrt(2);
if (type == 0) {
if (iscmpA) {
if (numblk == 1) {
svec1cmp(n,r2,A,irA,jcA,isspA,B,irB,jcB,isspB,AI,BI); }
else {
svec2cmp(n,numblk,cumblksize,blknnz,r2,A,irA,jcA,isspA,B,irB,jcB,isspB,AI,BI);
}
} else {
if (numblk == 1) {
svec1(n,r2,A,irA,jcA,isspA,B,irB,jcB,isspB); }
else {
svec2(n,numblk,cumblksize,blknnz,r2,A,irA,jcA,isspA,B,irB,jcB,isspB);
}
}
} else {
if (iscmpA) {
if (numblk == 1) {
svec3cmp(n,r2,A,irA,jcA,isspA,B,irB,jcB,isspB,AI,BI); }
else {
svec4cmp(n,numblk,cumblksize,blknnz,r2,A,irA,jcA,isspA,B,irB,jcB,isspB,AI,BI);
}
} else {
if (numblk == 1) {
svec3(n,r2,A,irA,jcA,isspA,B,irB,jcB,isspB); }
else {
svec4(n,numblk,cumblksize,blknnz,r2,A,irA,jcA,isspA,B,irB,jcB,isspB);
}
}
}
return;
}
// Sample factor vectors
// Function written from perspective of sampling user factor vectors with cross-topics
// Switch roles of user-item inputs to sample item factor vectors
void sampleTopicFactorVectors(uint32_t* items, double* resids, const mxArray* exampsByUser,
int KU, int KM, int numUsers, int numItems, double invSigmaSqd,
ptrdiff_t numTopicFacs, double* LambdaU, double* muU, double* c, double* d,
uint32_t* zU, uint32_t* zM){
// Array of random number generators
gsl_rng** rngs = getRngArray();
// Extract internals of jagged arrays
uint32_t** userExamps;
mwSize* userLens;
unpackJagged(exampsByUser, &userExamps, &userLens, numUsers);
ptrdiff_t numTopicFacsSqd = numTopicFacs*numTopicFacs;
ptrdiff_t numTopicFacsTimesNumItems = numTopicFacs*numItems;
ptrdiff_t numTopicFacsTimesNumUsers = numTopicFacs*numUsers;
// BLAS constants
char uplo[] = "U";
char trans[] = "N";
char diag[] = "N";
ptrdiff_t oneInt = 1;
double oneDbl = 1;
double zeroDbl = 0;
// Compute muBase = LambdaU*muU
double* muBase = mxMalloc(numTopicFacs*sizeof(*muBase));
dsymv(uplo, &numTopicFacs, &oneDbl, LambdaU, &numTopicFacs, muU, &oneInt, &zeroDbl, muBase, &oneInt);
// Allocate memory for new mean and precision parameters
double** muNew[MAX_NUM_THREADS];
double** LambdaNew[MAX_NUM_THREADS];
for(int thread = 0; thread < MAX_NUM_THREADS; thread++){
muNew[thread] = mxMalloc(KM*sizeof(**muNew));
LambdaNew[thread] = mxMalloc(KM*sizeof(**LambdaNew));
for(int i = 0; i < KM; i++){
muNew[thread][i] = mxMalloc(numTopicFacs*sizeof(***muNew));
LambdaNew[thread][i] = mxMalloc(numTopicFacsSqd*sizeof(***LambdaNew));
}
}
#pragma omp parallel for
for(int u = 0; u < numUsers; u++){
int thread = omp_get_thread_num();
for(int i = 0; i < KM; i++){
// Initialize new mean to muBase
dcopy(&numTopicFacs, muBase, &oneInt, muNew[thread][i], &oneInt);
// Initialize new precision to LambdaU
dcopy(&numTopicFacsSqd, LambdaU, &oneInt, LambdaNew[thread][i], &oneInt);
}
// Iterate over user's examples
mxArray* exampsArray = mxGetCell(exampsByUser, u);
mwSize len = mxGetN(exampsArray);
uint32_t* examps = (uint32_t*) mxGetData(exampsArray);
for(int j = 0; j < len; j++){
uint32_t e = examps[j]-1;
int m = items[e]-1;
int userTop = zU[e]-1;
int itemTop = zM[e]-1;
// Item vector for this rated item
double* dVec = d + m*numTopicFacs + userTop*numTopicFacsTimesNumItems;
// Compute posterior sufficient statistics for factor vector
// Add resid * dVec/sigmaSqd to muNew
double resid = resids[e];
resid *= invSigmaSqd;
daxpy(&numTopicFacs, &resid, dVec, &oneInt, muNew[thread][itemTop], &oneInt);
// Add (dVec * dVec^t)/sigmaSqd to LambdaNew
// Exploit symmetric structure of LambdaNew
dsyr(uplo, &numTopicFacs, &invSigmaSqd, dVec, &oneInt, LambdaNew[thread][itemTop],
&numTopicFacs);
}
for(int i = 0; i < KM; i++){
// Compute upper Cholesky factor of LambdaNew
ptrdiff_t info;
dpotrf(uplo, &numTopicFacs, LambdaNew[thread][i], &numTopicFacs, &info);
// Solve for (LambdaNew)^-1*muNew using Cholesky factor
dpotrs(uplo, &numTopicFacs, &oneInt, LambdaNew[thread][i], &numTopicFacs, muNew[thread][i],
&numTopicFacs, &info);
// Sample vector of N(0,1) variables
gsl_rng* rng = rngs[thread];
double* cVec = c + u*numTopicFacs + i*numTopicFacsTimesNumUsers;
for(int f = 0; f < numTopicFacs; f++)
cVec[f] = gsl_ran_gaussian(rng, 1);
// Solve for (chol(LambdaNew,'U'))^-1*N(0,1)
dtrtrs(uplo, trans, diag, &numTopicFacs, &oneInt, LambdaNew[thread][i],
&numTopicFacs, cVec, &numTopicFacs, &info);
// Add muNew to aVec
daxpy(&numTopicFacs, &oneDbl, muNew[thread][i], &oneInt, cVec, &oneInt);
}
}
// Clean up
mxFree(userExamps);
mxFree(userLens);
mxFree(muBase);
for(int thread = 0; thread < MAX_NUM_THREADS; thread++){
for(int i = 0; i < KM; i++){
mxFree(muNew[thread][i]);
mxFree(LambdaNew[thread][i]);
}
mxFree(muNew[thread]);
mxFree(LambdaNew[thread]);
}
}
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
// printf("start of file \n");
// Get array_sizes
const mxArray* mx_array_sizes = mexGetVariablePtr("global", "array_sizes");
if (mx_array_sizes == NULL) {
mexErrMsgTxt("array_sizes not defined");
}
unsigned array_sizes = (unsigned)mxGetScalar(mx_array_sizes);
// Get iteration
const mxArray* mx_iteration = mexGetVariablePtr("caller", "iteration");
if (mx_iteration == NULL) {
mexErrMsgTxt("iteration not defined");
}
double iteration = mxGetScalar(mx_iteration);
// Get protection_time
const mxArray* mx_protection_time = mexGetVariablePtr("caller", "protection_time");
if (mx_protection_time == NULL) {
mexErrMsgTxt("protection_time not defined");
}
double protection_time = mxGetScalar(mx_protection_time);
// Get join_probability
const mxArray* mx_join_probability = mexGetVariablePtr("caller", "join_probability");
if (mx_join_probability == NULL) {
mexErrMsgTxt("join_probability not defined");
}
double join_probability = mxGetScalar(mx_join_probability);
// Get threshold_join_nodes
const mxArray* mx_threshold_join_nodes = mexGetVariablePtr("caller", "threshold_join_nodes");
if (mx_threshold_join_nodes == NULL) {
mexErrMsgTxt("threshold_join_nodes not defined");
}
double threshold_join_nodes = mxGetScalar(mx_threshold_join_nodes);
// Get time
const mxArray* mx_time = mexGetVariablePtr("global", "time");
if (mx_time == NULL) {
mexErrMsgTxt("time not defined");
}
double time = mxGetScalar(mx_time);
unsigned width_cell_store = mxGetN(prhs[1]);
unsigned no_cells = mxGetM(prhs[2]);
unsigned no_FEM_elements = mxGetM(prhs[5]);
unsigned length_FEM_node_positions = mxGetM(prhs[6]);
double* initial_cell_store = mxGetPr(prhs[1]);
double* initial_cells_per_node = mxGetPr(prhs[3]);
double* initial_Dpp = mxGetPr(prhs[4]);
double* initial_FEM_elements = mxGetPr(prhs[5]);
double* initial_previous_FEM_node_positions = mxGetPr(prhs[6]);
double* initial_node_positions = mxGetPr(prhs[7]);
double* initial_time_nodes_created = mxGetPr(prhs[8]);
plhs[0] = mxCreateCellMatrix(no_cells, 1);
plhs[1] = mxCreateDoubleMatrix(array_sizes, width_cell_store, mxREAL);
plhs[2] = mxCreateCellMatrix(no_cells, 1);
plhs[3] = mxCreateDoubleMatrix(array_sizes, 1, mxREAL);
plhs[4] = mxCreateDoubleMatrix(length_FEM_node_positions, 1, mxREAL);
plhs[5] = mxCreateDoubleMatrix(no_FEM_elements, 3, mxREAL);
plhs[6] = mxCreateDoubleMatrix(length_FEM_node_positions, 2, mxREAL);
plhs[7] = mxCreateDoubleMatrix(array_sizes, 2, mxREAL);
plhs[8] = mxCreateDoubleMatrix(array_sizes, 1, mxREAL);
plhs[9] = mxCreateDoubleMatrix(1, 1, mxREAL);
double* final_cell_store = mxGetPr(plhs[1]);
double* final_cells_per_node = mxGetPr(plhs[3]);
double* final_Dpp = mxGetPr(plhs[4]);
double* final_FEM_elements = mxGetPr(plhs[5]);
double* final_previous_FEM_node_positions = mxGetPr(plhs[6]);
double* final_node_positions = mxGetPr(plhs[7]);
double* final_time_nodes_created = mxGetPr(plhs[8]);
double* no_join_nodes_this_iteration = mxGetPr(plhs[9]);
*no_join_nodes_this_iteration = 0;
// set output matrices equal to input matrices
for(unsigned current_node=0;current_node<array_sizes;current_node++){
final_cells_per_node[current_node] = initial_cells_per_node[current_node];
final_time_nodes_created[current_node] = initial_time_nodes_created[current_node];
for(unsigned dim=0;dim<2;dim++){
final_node_positions[current_node+array_sizes*dim] = initial_node_positions[current_node+array_sizes*dim];
}
for(unsigned i=0;i<width_cell_store;i++){
final_cell_store[current_node+i*array_sizes] = initial_cell_store[current_node+i*array_sizes];
}
}
for(unsigned current_element=0;current_element<no_FEM_elements;current_element++){
for(unsigned i=0;i<3;i++){
final_FEM_elements[current_element+no_FEM_elements*i] =
initial_FEM_elements[current_element+no_FEM_elements*i];
}
}
for(unsigned current_FEM_node=0;current_FEM_node<length_FEM_node_positions;current_FEM_node++){
final_Dpp[current_FEM_node] = initial_Dpp[current_FEM_node];
for(unsigned dim=0;dim<2;dim++){
final_previous_FEM_node_positions[current_FEM_node+length_FEM_node_positions*dim] =
initial_previous_FEM_node_positions[current_FEM_node+length_FEM_node_positions*dim];
}
}
// set output cells equal to input cells
for(unsigned current_cell=0; current_cell<no_cells; current_cell++) {
mxArray* mx_initial_cell_nodes = mxGetCell(prhs[2], current_cell);
unsigned no_cell_nodes = mxGetN(mx_initial_cell_nodes);
double* initial_cell_nodes = mxGetPr(mx_initial_cell_nodes);
mxArray* mx_final_cell_nodes = mxCreateDoubleMatrix(1, no_cell_nodes, mxREAL);
double* final_cell_nodes = mxGetPr(mx_final_cell_nodes);
mxArray* mx_initial_cell_elements = mxGetCell(prhs[0], current_cell);
double* initial_cell_elements = mxGetPr(mx_initial_cell_elements);
mxArray* mx_final_cell_elements = mxCreateDoubleMatrix(1, no_cell_nodes, mxREAL);
double* final_cell_elements = mxGetPr(mx_final_cell_elements);
for(unsigned i=0; i<no_cell_nodes;i++){
final_cell_nodes[i] = initial_cell_nodes[i];
final_cell_elements[i] = initial_cell_elements[i];
}
mxSetCell(plhs[2], current_cell, mx_final_cell_nodes);
mxSetCell(plhs[0], current_cell, mx_final_cell_elements);
}
bool join_logical;
// loop over all cells
for(unsigned current_cell_ci=0; current_cell_ci<no_cells; current_cell_ci++) {
join_logical = false;
// printf("start of main loop \n");
unsigned current_cell_mi = current_cell_ci+1;
mxArray* mx_cell_nodes = mxGetCell(plhs[2], current_cell_ci);
double* cell_nodes = mxGetPr(mx_cell_nodes);
unsigned no_cell_nodes = mxGetN(mx_cell_nodes);
// only proceed if there are more than 3 cell nodes
if(no_cell_nodes > 3){
// loop over the nodes of the current cell
for(unsigned current_node_local=0; current_node_local<no_cell_nodes; current_node_local++) {
double rand_number = rand()/((double)RAND_MAX);
// only proceed with p(join_probability)
if(rand_number < join_probability){
// find current node and clockwise node in matlab and c indicies
unsigned current_node_global_mi = (unsigned)cell_nodes[current_node_local];
unsigned current_node_global_ci = current_node_global_mi-1;
unsigned clockwise_node_local = (current_node_local+1)%no_cell_nodes;
unsigned clockwise_node_global_mi = (unsigned)cell_nodes[clockwise_node_local];
unsigned clockwise_node_global_ci = clockwise_node_global_mi - 1;
// extract the positions of the current node and clockwise node from the node positions matrix
double current_node_position[2], clockwise_node_position[2];
for(unsigned dim=0;dim<2;dim++) {
current_node_position[dim] = final_node_positions[current_node_global_ci + dim*array_sizes];
clockwise_node_position[dim] = final_node_positions[clockwise_node_global_ci + dim*array_sizes];
}
// find the current edge length
double current_edge_length = findStraightLineDistanceBetweenTwoNodes(current_node_position,
clockwise_node_position);
// only proceed if edge length is less than threshold, and nodes have not been created very
// recently
if(current_edge_length < threshold_join_nodes &&
(time-final_time_nodes_created[current_node_global_ci])>protection_time &&
(time-final_time_nodes_created[clockwise_node_global_ci])>protection_time){
// printf("hello \n");
// look for a cell that shares the edge - we need this for a T1 swap
bool cell_with_same_edge_found = false;
int cell_with_same_edge_mi = -1;
unsigned counter_1 = 0;
// loop over all cells containing current_node_global
for(unsigned i=0;i<final_cells_per_node[current_node_global_ci];i++){
unsigned temp_cell_1_mi = (unsigned)final_cell_store[current_node_global_ci + i*array_sizes];
// if not current_cell, loop over all cells containing clockwise_node_global
if(temp_cell_1_mi != current_cell_mi && !cell_with_same_edge_found){
for(unsigned j=0;j<final_cells_per_node[clockwise_node_global_ci];j++){
unsigned temp_cell_2_mi = (unsigned)final_cell_store[clockwise_node_global_ci + j*array_sizes];
// if cell containing clockwise_node_global is also a cell containing current_node_global,
// but not current_cell, then it is cell_with_same_edge;
if(temp_cell_2_mi == temp_cell_1_mi){
cell_with_same_edge_mi = temp_cell_1_mi;
cell_with_same_edge_found = true;
break;
}
}
}
}
if(!cell_with_same_edge_found){
join_logical = true;
(*no_join_nodes_this_iteration)++;
// printf("doing a join \n");
double new_node_position[2];
for(unsigned dim=0;dim<2;dim++) {
new_node_position[dim] = (current_node_position[dim] +
clockwise_node_position[dim])/2;
}
// find two unused nodes to put new nodes in
unsigned new_node_ci = 0;
while(final_cells_per_node[new_node_ci]>0){
new_node_ci++;
}
unsigned new_node_mi = new_node_ci+1;
assert(new_node_mi <= array_sizes);
// store new node position
for(unsigned dim=0;dim<2;dim++){
final_node_positions[new_node_ci+dim*array_sizes] =
new_node_position[dim];
}
// set time new nodes created to current time
final_time_nodes_created[new_node_ci] = time;
// edit current cell nodes to contain new node instead of previous two nodes
mxArray* mx_cell_nodes_edited = mxCreateDoubleMatrix(1, no_cell_nodes-1, mxREAL);
double* cell_nodes_edited = mxGetPr(mx_cell_nodes_edited);
int temp_counter = -1;
for(unsigned temp_current_node_local=0;temp_current_node_local<no_cell_nodes;temp_current_node_local++){
unsigned temp_current_node_global_mi = (unsigned)cell_nodes[temp_current_node_local];
if(temp_current_node_global_mi==current_node_global_mi){
temp_counter++;
cell_nodes_edited[temp_counter]=new_node_mi;
}
else if(temp_current_node_global_mi==clockwise_node_global_mi){}
else{
temp_counter++;
cell_nodes_edited[temp_counter]=temp_current_node_global_mi;
}
}
mxSetCell(plhs[2], current_cell_ci, mx_cell_nodes_edited);
// printf("edited current cell \n");
final_cells_per_node[new_node_ci] = 1;
final_cell_store[new_node_ci] = current_cell_mi;
if(final_cells_per_node[current_node_global_ci] > 1.1){
for(unsigned i=0;i<final_cells_per_node[current_node_global_ci];i++){
unsigned temp_cell_mi = (unsigned)final_cell_store[current_node_global_ci + i*array_sizes];
if(temp_cell_mi!=current_cell_mi){
unsigned temp_cell_ci = temp_cell_mi-1;
mxArray* mx_cell_nodes_temp_cell = mxGetCell(plhs[2], temp_cell_ci);
double* cell_nodes_temp_cell = mxGetPr(mx_cell_nodes_temp_cell);
unsigned no_cell_nodes_temp_cell = mxGetN(mx_cell_nodes_temp_cell);
mxArray* mx_cell_nodes_temp_cell_edited = mxCreateDoubleMatrix(1, no_cell_nodes_temp_cell, mxREAL);
double* cell_nodes_temp_cell_edited = mxGetPr(mx_cell_nodes_temp_cell_edited);
for(unsigned temp_current_node_local=0;temp_current_node_local<no_cell_nodes_temp_cell;temp_current_node_local++){
unsigned temp_current_node_global_mi = (unsigned)cell_nodes_temp_cell[temp_current_node_local];
if(temp_current_node_global_mi==current_node_global_mi){
cell_nodes_temp_cell_edited[temp_current_node_local] = new_node_mi;
}
else{
cell_nodes_temp_cell_edited[temp_current_node_local] = temp_current_node_global_mi;
}
}
mxSetCell(plhs[2], temp_cell_ci, mx_cell_nodes_temp_cell_edited);
final_cells_per_node[new_node_ci]++;
unsigned matrix_index = (unsigned)(new_node_ci+array_sizes*(final_cells_per_node[new_node_ci]-1));
final_cell_store[matrix_index] = temp_cell_mi;
}
}
// printf("edited cells with node 1 \n");
}
if(final_cells_per_node[clockwise_node_global_ci] > 1.1){
for(unsigned i=0;i<final_cells_per_node[clockwise_node_global_ci];i++){
unsigned temp_cell_mi = (unsigned)final_cell_store[clockwise_node_global_ci + i*array_sizes];
if(temp_cell_mi!=current_cell_mi){
unsigned temp_cell_ci = temp_cell_mi-1;
// edit stretch cell 1 by adding in two new nodes in place of current node global
mxArray* mx_cell_nodes_temp_cell = mxGetCell(plhs[2], temp_cell_ci);
double* cell_nodes_temp_cell = mxGetPr(mx_cell_nodes_temp_cell);
unsigned no_cell_nodes_temp_cell = mxGetN(mx_cell_nodes_temp_cell);
mxArray* mx_cell_nodes_temp_cell_edited = mxCreateDoubleMatrix(1, no_cell_nodes_temp_cell, mxREAL);
double* cell_nodes_temp_cell_edited = mxGetPr(mx_cell_nodes_temp_cell_edited);
for(unsigned temp_current_node_local=0;temp_current_node_local<no_cell_nodes_temp_cell;temp_current_node_local++){
unsigned temp_current_node_global_mi = (unsigned)cell_nodes_temp_cell[temp_current_node_local];
if(temp_current_node_global_mi==clockwise_node_global_mi){
cell_nodes_temp_cell_edited[temp_current_node_local] = new_node_mi;
}
else{
cell_nodes_temp_cell_edited[temp_current_node_local] = temp_current_node_global_mi;
}
}
mxSetCell(plhs[2], temp_cell_ci, mx_cell_nodes_temp_cell_edited);
// add stretch cell 1 to cells_per_node and cell_store for new_node and new_node_2
final_cells_per_node[new_node_ci]++;
unsigned matrix_index = (unsigned)(new_node_ci+array_sizes*(final_cells_per_node[new_node_ci]-1));
final_cell_store[matrix_index] = temp_cell_mi;
}
}
printf("edited cells with node 2 \n");
}
// reset cells per node and cell store for current_node_global and clockwise_node_global.
// they should no longer be part of any cells, unless something has gone horribly wrong.
final_cells_per_node[current_node_global_ci] = 0;
final_cells_per_node[clockwise_node_global_ci] = 0;
for(unsigned i=0;i<width_cell_store;i++){
final_cell_store[current_node_global_ci+i*array_sizes] = 0;
final_cell_store[clockwise_node_global_ci+i*array_sizes] = 0;
}
for(unsigned dim=0;dim<2;dim++){
final_node_positions[current_node_global_ci+dim*array_sizes] = 0;
final_node_positions[clockwise_node_global_ci+dim*array_sizes] = 0;
}
}
}
}
if(join_logical){break;}
}
}
if(join_logical){break;}
}
}
