template <> bool DataOutputNode<lbfloat>::mat_write(std::string file_path, std::string var_name)
{
//Copy data to buffer
lbfloat* buf = nullptr;
size_t buf_size;
contract(buf,buf_size,false);
std::cout << "Output matrix will be [" << _n_samples << "] x [" << _n_channels << "]." << std::endl;
//setup the output
mat_t *mat;
matvar_t *matvar;
size_t dims[2] = {_n_samples,_n_channels};
mat = Mat_Open(file_path.c_str(),MAT_ACC_RDWR);
if(mat)
{
//output matrix
matvar = Mat_VarCreate(var_name.c_str(),MAT_C_DOUBLE,MAT_T_DOUBLE,2,dims,buf,0);
Mat_VarWrite(mat, matvar, MAT_COMPRESSION_NONE);
Mat_Close(mat);
Mat_VarFree(matvar);
std::cout << "Output data to " << var_name << " variable in file " << file_path << "!" << std::endl;
delete [] buf;
return true;
}
std::cerr << "Couldn't output to file." << std::endl;
delete [] buf;
return false;
}
static np::ndarray bnread( const std::string & name ) {
np::ndarray r(np::empty(make_tuple(0), np::dtype::get_builtin<unsigned char>()));
mat_t * mat = Mat_Open(name.c_str(),MAT_ACC_RDONLY);
if(mat)
{
matvar_t * gt = Mat_VarRead( mat, (char*)"groundTruth" );
if(!gt)
return r;
int nSeg = gt->dims[1];
if(!nSeg)
return r;
for( int s = 0; s < nSeg; s++ ) {
matvar_t * cl = Mat_VarGetCell(gt, s);
matvar_t * bnd = Mat_VarGetStructField( cl, (void*)"Boundaries", MAT_BY_NAME, 0 );
int W = bnd->dims[1], H = bnd->dims[0];
if( bnd->data_type != MAT_T_UINT8 )
printf("Unexpected boundary type! Continuing in denial and assuming uint8_t\n");
if( r.shape(0) <= 0 )
r = np::empty(make_tuple(nSeg,H,W), np::dtype::get_builtin<unsigned char>());
assert( r.shape(1) == H && r.shape(2) == W );
const unsigned char * pdata = static_cast<const unsigned char*>(bnd->data);
unsigned char * pr = reinterpret_cast<unsigned char*>(r.get_data()+s*W*H);
for( int j=0; j<H; j++ )
for( int i=0; i<W; i++ )
pr[j*W+i] = pdata[i*H+j];
}
Mat_VarFree( gt );
Mat_Close(mat);
}
return r;
}
static std::tuple< std::vector<RMatrixXs>, std::vector<RMatrixXb> > readMat( const std::string & name ) {
std::vector<RMatrixXs> seg;
std::vector<RMatriXb> bnd;
mat_t * mat = Mat_Open(name.c_str(),MAT_ACC_RDONLY);
if(mat)
{
matvar_t * gt = Mat_VarRead( mat, (char*)"groundTruth" );
if(!gt)
return std::make_tuple(seg,bnd);
int nSeg = gt->dims[1];
if(!nSeg)
return std::make_tuple(seg,bnd);
for( int s = 0; s < nSeg; s++ ) {
const char * names[2] = {"Segmentation","Boundaries"};
const int types[2] = {MAT_T_UINT16,MAT_T_UINT8};
for( int it=0; it<2; it++ ) {
matvar_t * cl = Mat_VarGetCell(gt, s);
matvar_t * arr = Mat_VarGetStructField( cl, (void*)names[it], MAT_BY_NAME, 0 );
int W = arr->dims[1], H = arr->dims[0];
if( arr->data_type != types[it] )
printf("Unexpected %s type! Continuing in denial ...\n",names[it]);
if(it==0)
seg.push_back( MatrixXus::Map((const uint16_t*)arr->data,H,W)-1 );
else
bnd.push_back( RMatrixXb::Map((const bool*)arr->data,H,W) );
}
}
Mat_VarFree( gt );
Mat_Close(mat);
}
return std::make_tuple(seg,bnd);
}
/** \brief save Array-struct as MATLAB .mat file.
Currently, the function converts all arrays to
double-arrays. Should be easy to implement for arbitrary types if
needed.
\param a the Array
\param varname MATLAB-name of the array
\param file the filename
\param append if TRUE, the function tries to open() the file, else it is overwritten
\return error code
*/
int write_array_matlab( const Array *a, const char *varname, const char *file, bool append ){
mat_t *mfile;
matvar_t *marr=NULL;
int i;
if( append ){
if( !(mfile=Mat_Open( file, MAT_ACC_RDWR )) ){
errprintf("Could not open '%s', creating new file\n", file);
}
}
if( !mfile ){
if( !(mfile=Mat_Create( file, NULL )) ){
errprintf("Could not open '%s' for writing\n", file);
return -1;
}
}
int ndim = MAX(2, a->ndim);
int *size = (int*)malloc( ndim*sizeof(int));
if( a->ndim==1 ){
size[0]=1;
size[1]=a->size[0];
} else {
memcpy( size, a->size, ndim*sizeof(int));
}
dprintf("Writing to file '%s' variable '%s', ndim=%i\n", file, varname, ndim);
/* convert to column major for MATLAB */
Array *b=array_convert_rowcolmajor( (Array*)a, TRUE );
dprintf("Up-cast, b->ndim=%i, b->size=%p, b->size[0]=%i\n", b->ndim, b->size, b->size[0]);
/* up-cast to DOUBLE - copy of b */
Array *c=array_new( DOUBLE, b->ndim, b->size );
dprintf("casting\n");
for( i=0; i<array_NUMEL(b); i++ ){
array_dtype_to_double( array_INDEXMEM1(c,i), array_INDEXMEM1(b,i), b->dtype );
}
array_free( b );
dprintf("Creating MATLAB-rep\n");
marr = Mat_VarCreate( varname, MAT_C_DOUBLE, MAT_T_DOUBLE,
ndim, size, c->data, MEM_CONSERVE /* Array remains owner */
);
dprintf("mfile=%p, marr=%p, rank=%i,\n", mfile, marr, marr->rank );
int succ=Mat_VarWrite( mfile, marr, 0 );
dprintf("done writing with succ=%i\n", succ);
Mat_Close( mfile );
Mat_VarFree( marr );
array_free( c );
free( size );
return 0;
}
/*
* matWrite - write signals from measurement structure to MAT file
*/
int matWrite(measurement_t *measurement, const char *outFileName)
{
size_t dims[2];
int err = 0;
mat_t *mat;
matvar_t *matvar;
mat = Mat_Create(outFileName, NULL);
if (mat != NULL) {
/* loop over all time series */
struct hashtable *timeSeriesHash = measurement->timeSeriesHash;
/* Iterator constructor only returns a valid iterator if
* the hashtable is not empty */
if (hashtable_count(timeSeriesHash) > 0) {
struct hashtable_itr *itr = hashtable_iterator(timeSeriesHash);
do {
char *signalName = hashtable_iterator_key(itr);
timeSeries_t *timeSeries = hashtable_iterator_value(itr);
double *timeValue = (double *)malloc(sizeof(double)*2*timeSeries->n);
unsigned int i;
/*
* build up a 1x2n array with time stamps in [0..n-1] and
* values in [n..2n-1].
*/
for(i=0;i<timeSeries->n;i++) {
timeValue[i] = timeSeries->time[i];
}
for(i=0;i<timeSeries->n;i++) {
timeValue[timeSeries->n + i] = timeSeries->value[i];
}
dims[0] = timeSeries->n;
dims[1] = 2;
/* output signal to mat structure and free up temp array. */
matvar = Mat_VarCreate(signalName, MAT_C_DOUBLE, MAT_T_DOUBLE,
2, dims, timeValue, 0);
Mat_VarWrite(mat, matvar, 0);
Mat_VarFree(matvar);
free(timeValue);
} while (hashtable_iterator_advance(itr));
free(itr);
}
Mat_Close(mat);
} else {
fprintf(stderr, "error: could not create MAT file %s\n", outFileName);
err = 1;
}
return err;
}
static int
ismat( const char *filename )
{
mat_t *mat;
if( !(mat = Mat_Open( filename, MAT_ACC_RDONLY )) )
return( 0 );
Mat_Close( mat );
return( 1 );
}
int
vips__mat_ismat( const char *filename )
{
mat_t *mat;
vips_error_freeze();
mat = Mat_Open( filename, MAT_ACC_RDONLY );
Mat_Close( mat );
vips_error_thaw();
return( mat != NULL );
}
double *read_mat(const char *filename, const char *varname, size_t *dims)
{
mat_t *mat;
matvar_t *var;
double *array;
size_t nbytes;
mat = Mat_Open(filename, MAT_ACC_RDONLY);
if (!mat) {
fprintf(stderr, "Error opening MAT file \"%s\"!\n", filename);
exit(EXIT_FAILURE);
}
var = Mat_VarRead(mat, varname);
if (!var) {
fprintf(stderr, "Error reading the variable %s.\n", varname);
Mat_Close(mat);
exit(EXIT_FAILURE);
}
if (var->data_type != MAT_T_DOUBLE || var->class_type != MAT_C_DOUBLE
|| var->rank != 2) {
fprintf(stderr, "%s is not a double-precision matrix.\n", varname);
Mat_VarFree(var);
Mat_Close(mat);
exit(EXIT_FAILURE);
}
nbytes = var->dims[0] * var->dims[1] * sizeof(double);
array = (double *)malloc(nbytes);
memcpy(array, var->data, nbytes);
memcpy(dims, var->dims, 2 * sizeof(size_t));
Mat_VarFree(var);
Mat_Close(mat);
return array;
}
// save a .mat matlab matrix
// will store a single matrix (sparse or dense) in a .mat file
// returns 0 on success
static
int write_mat(char const *const filename,
matrix_t *const A) {
#ifndef HAVE_MATIO
return 1;
#else
const char created_by[] = "created by " PACKAGE_STRING; // "created by Meagre-Crowd x.y.z"
mat_t* matfp;
matfp = Mat_Create(filename, created_by);
if(matfp == NULL)
return 1; // failed to open file
// create a matrix convert into
matvar_t* t = NULL;
int ret = 0;
if(A->format == DCOL || A->format == DROW) { // dense
ret = convert_matrix(A, DCOL, FIRST_INDEX_ZERO); // DROW -> DCOL if DROW
if(ret != 0)
ret = 2; // conversion failure
if(ret == 0) {
// TODO check for integer overflow in cast from unsigned int -> int
size_t dims[] = { A->m, A->n };
t = Mat_VarCreate( "x",
MAT_C_DOUBLE,
MAT_T_DOUBLE,
2, // always at least rank 2
dims,
A->dd,
0 // MAT_F_COMPLEX if complex, could avoid copying data: MAT_F_DONT_COPY_DATA if not sparse
);
if(t == NULL) {
ret = 3; // failed to malloc data for storage
}
else {
ret = Mat_VarWrite(matfp, t, 1); // compress
if(ret != 0)
ret = 4; // failed data write
}
}
}
else { // sparse
assert(0); // do we ever get sparse results?
}
Mat_Close(matfp);
Mat_VarFree(t);
return ret; // success?
#endif
}
void write_mat(const char *filename, const char *varname,
double *array, size_t *dims)
{
mat_t *mat;
matvar_t *var;
mat = Mat_CreateVer(filename, NULL, MAT_FT_DEFAULT);
if (!mat) {
fprintf(stderr, "Error creating MAT file \"%s\"\n", filename);
exit(EXIT_FAILURE);
}
var = Mat_VarCreate(varname, MAT_C_DOUBLE, MAT_T_DOUBLE,
2, dims, array, 0);
if (!var) {
fprintf(stderr, "Error creating variable %s.\n", varname);
Mat_Close(mat);
exit(EXIT_FAILURE);
}
Mat_VarWrite(mat, var, MAT_COMPRESSION_NONE);
Mat_VarFree(var);
Mat_Close(mat);
}
bool annoRead(std::string annoName, BOWImg &dst)
{
mat_t *matfp = Mat_Open(annoName.c_str(),MAT_ACC_RDONLY);
if(matfp == NULL)
{
std::cerr<<"Cannot open file '"<<annoName<<"'."<<std::endl;
return false;
}
char varName[] = "box_coord";
readNumber<int>(matfp,varName,dst.box);
//readNumber<double>(matfp,"obj_contour",dst.objContour);
Mat_Close(matfp);
return true;
}
TData read_data()
{
const char * fileName = "../data/mnist_uint8.mat";
TData res;
mat_t *mat = nullptr;
scope_guard _l([&mat, fileName](){
mat = Mat_Open(fileName, MAT_ACC_RDONLY);
},
[&mat](){Mat_Close(mat);});
if(!mat){
std::cout <<"cannot open "<<fileName<<std::endl;
return res;
}
matvar_t *var = 0;
int read_items = 0;
while((var = Mat_VarReadNextInfo(mat)) != nullptr){
if(strcmp(var->name, "train_x") == 0)
{
res.train_x = read_matrix_in_mat(mat, var->name);
read_items ++ ;
}
else if(strcmp(var->name, "train_y") == 0)
{
res.train_y = read_matrix_in_mat(mat, var->name);
read_items ++;
}
else if(strcmp(var->name, "test_x") == 0)
{
res.test_x = read_matrix_in_mat(mat, var->name);
read_items ++;
}
else if(strcmp(var->name, "test_y" ) == 0)
{
res.test_y = read_matrix_in_mat(mat, var->name);
read_items ++;
}
else{
//nothing here, just for fun...
}
Mat_VarFree(var);
}
if(read_items != 4)
{
std::cout<<"ooooooops, cannot read "<< fileName<<std::endl;
}
return res;
}
template <> bool DataOutputNode<lbcomplex>::mat_write(std::string file_path, std::string var_name)
{
//Copy data to buffer
lbcomplex* buf = nullptr;
size_t buf_size;
contract(buf,buf_size,false);
std::cout << "Output matrix will be [" << _n_samples << "] x [" << _n_channels << "]." << std::endl;
//setup the output
mat_t *mat;
matvar_t *matvar;
mat_complex_split_t data;
data.Re = malloc(buf_size*sizeof(lbfloat));
data.Im = malloc(buf_size*sizeof(lbfloat));
for(size_t ii=0; ii<buf_size; ++ii)
{
reinterpret_cast<lbfloat*>(data.Re)[ii] = std::real(buf[ii]);
reinterpret_cast<lbfloat*>(data.Im)[ii] = std::imag(buf[ii]);
}
size_t dims[2] = {_n_samples,_n_channels};
mat = Mat_Open(file_path.c_str(),MAT_ACC_RDWR);
if(mat)
{
//output matrix
matvar = Mat_VarCreate(var_name.c_str(),MAT_C_DOUBLE,MAT_T_DOUBLE,2,dims,&data,MAT_F_COMPLEX);
Mat_VarWrite(mat, matvar, MAT_COMPRESSION_NONE);
Mat_Close(mat);
Mat_VarFree(matvar);
std::cout << "Output data to " << var_name << " variable in file " << file_path << "!" << std::endl;
delete [] buf;
return true;
}
std::cerr << "Couldn't output to file." << std::endl;
delete [] buf;
return false;
}
// Default destructor
MatFileIO::~MatFileIO() {
Mat_Close(mat);
}
int main (int argc, char *argv[]){
char **str2,*line,*curr;
const char* ext=".exo";
int
i,j,k,n,n1,cpu_word_size,io_word_size,exo_file,
num_axes,num_nodes,num_elements,num_blocks,
num_side_sets,num_node_sets,num_time_steps,
num_global_vars,
num_nodal_vars,num_element_vars,*ids,*iscr,
*nsssides,*nssdfac,*elem_list,*side_list,
*nnsnodes,*nnsdfac,*node_list;
double
*scr,*x,*y,*z,
*escr;
char * blknames = NULL;
int *num_elem_in_block = NULL;
/* QA Info */
printf("%s: %s, %s\n", qainfo[0], qainfo[2], qainfo[1]);
/* usage message*/
if(argc != 2){
printf("%s matlab_file_name.\n",argv[0]);
printf(" the matlab_file_name is required\n");
printf("%d", argc);
exit(1);
}
/*open input file*/
mat_file = Mat_Open(argv[1], MAT_ACC_RDONLY);
if (mat_file == NULL) {
printf("Error opening matlab file %s\n", argv[1]);
return(1);
}
/*open output file*/
cpu_word_size=sizeof(double);
io_word_size=sizeof(double);
/* QA records */
ext=".exo";
line = (char *) calloc (2049,sizeof(char));
strcpy(line,argv[1]);
strtok(line,".");
strcat(line,ext);
exo_file = ex_create(line,EX_CLOBBER,&cpu_word_size,&io_word_size);
if (exo_file < 0){
printf("error creating %s\n",line);
exit(1);
}
/* print */
fprintf(stderr,"translating %s to %s ... ",argv[1],line);
/* read database parameters */
matGetInt("naxes", 1, 1,&num_axes);
matGetInt("nnodes", 1, 1,&num_nodes);
matGetInt("nelems", 1, 1,&num_elements);
matGetInt("nblks", 1, 1,&num_blocks);
matGetInt("nnsets", 1, 1,&num_node_sets);
matGetInt("nssets", 1, 1,&num_side_sets);
matGetInt("nsteps", 1, 1,&num_time_steps);
matGetInt("ngvars", 1, 1,&num_global_vars);
matGetInt("nnvars", 1, 1,&num_nodal_vars);
matGetInt("nevars", 1, 1,&num_element_vars);
/*export parameters */
ex_put_init(exo_file,line,
num_axes,num_nodes,num_elements,num_blocks,
num_node_sets,num_side_sets);
free(line);
if ( num_global_vars > 0 ){
ex_put_variable_param(exo_file,EX_GLOBAL,num_global_vars);
}
if ( num_nodal_vars > 0 ){
ex_put_variable_param(exo_file,EX_NODAL,num_nodal_vars);
}
if ( num_element_vars > 0 ){
ex_put_variable_param(exo_file,EX_ELEM_BLOCK,num_element_vars);
}
/* nodal coordinates */
x = (double *) calloc(num_nodes,sizeof(double));
y = (double *) calloc(num_nodes,sizeof(double));
if (num_axes == 3)
z = (double *) calloc(num_nodes,sizeof(double));
else
z = NULL;
matGetDbl("x0", num_nodes, 1, x);
matGetDbl("y0", num_nodes, 1, y);
if (num_axes == 3)
matGetDbl("z0", num_nodes,1,z);
ex_put_coord(exo_file,x,y,z);
free(x);
free(y);
if (num_axes == 3){
free(z);
}
/* side sets (section by dgriffi) */
if(num_side_sets > 0){
/* ssids */
ids = (int *) calloc(num_side_sets,sizeof(int));
matGetInt("ssids",num_side_sets, 1,ids);
/* nsssides */
nsssides = (int *) calloc(num_side_sets,sizeof(int));
matGetInt("nsssides",num_side_sets,1,nsssides);
/* nssdfac */
nssdfac = (int *) calloc(num_side_sets,sizeof(int));
matGetInt("nssdfac",num_side_sets,1,nssdfac);
for(i=0;i<num_side_sets;i++){
char name[32];
ex_put_set_param(exo_file,EX_SIDE_SET,ids[i],nsssides[i],nssdfac[i]);
elem_list = (int *) calloc(nsssides[i],sizeof(int));
side_list = (int *) calloc(nsssides[i],sizeof(int));
escr = (double *) calloc(nssdfac[i],sizeof(double));
sprintf(name,"sselem%02d",i+1);
matGetInt(name,nsssides[i],1,elem_list);
sprintf(name,"ssside%02d",i+1);
matGetInt(name,nsssides[i],1,side_list);
ex_put_set(exo_file,EX_SIDE_SET,ids[i],elem_list,side_list);
free(elem_list);
free(side_list);
sprintf(name,"ssfac%02d",i+1);
matGetDbl(name,nssdfac[i],1,escr);
ex_put_set_dist_fact(exo_file,EX_SIDE_SET,ids[i],escr);
free(escr);
}
free(nsssides);
free(nssdfac);
free(ids);
}
/* node sets (section by dgriffi) */
if(num_node_sets > 0){
/* nsids */
ids = (int *) calloc(num_node_sets,sizeof(int));
matGetInt("nsids",num_node_sets, 1,ids);
/* nnsnodes */
nnsnodes = (int *) calloc(num_node_sets,sizeof(int));
matGetInt("nnsnodes",num_node_sets,1,nnsnodes);
/* nnsdfac */
nnsdfac = (int *) calloc(num_node_sets,sizeof(int));
matGetInt("nnsdfac",num_node_sets,1,nnsdfac);
for(i=0;i<num_node_sets;i++){
char name[32];
ex_put_set_param(exo_file,EX_NODE_SET,ids[i],nnsnodes[i],nnsdfac[i]);
node_list = (int *) calloc(nnsnodes[i],sizeof(int));
escr = (double *) calloc(nnsdfac[i],sizeof(double));
sprintf(name,"nsnod%02d",i+1);
matGetInt(name,nnsnodes[i],1,node_list);
ex_put_set(exo_file,EX_NODE_SET,ids[i],node_list,NULL);
free(node_list);
sprintf(name,"nsfac%02d",i+1);
matGetDbl(name,nnsdfac[i],1,escr);
ex_put_set_dist_fact(exo_file,EX_NODE_SET,ids[i],escr);
free(escr);
}
free(nnsdfac);
free(nnsnodes);
free(ids);
}
/* element blocks */
/* get elem block ids */
ids = (int *) calloc(num_blocks,sizeof(int));
matGetInt("blkids",num_blocks,1,ids);
/* get elem block types */
blknames = (char *) calloc(num_blocks*(MAX_STR_LENGTH+1),sizeof(char));
matGetStr("blknames",blknames);
num_elem_in_block = (int *) calloc(num_blocks,sizeof(int));
curr = blknames;
curr = strtok(curr,"\n");
for(i=0;i<num_blocks;i++){
char name[32];
sprintf(name,"blk%02d",i+1);
n1 = matArrNRow(name);
n = matArrNCol(name);
iscr = (int *) calloc(n*n1,sizeof(int));
matGetInt(name,n1,n,iscr);
num_elem_in_block[i]=n;
ex_put_elem_block(exo_file,ids[i],curr,n,n1,0);
ex_put_conn(exo_file,EX_ELEM_BLOCK,ids[i],iscr,NULL,NULL);
free(iscr);
curr = strtok(NULL, "\n");
}
free(blknames);
/* time values */
if (num_time_steps > 0 ) {
scr = (double *) calloc(num_time_steps,sizeof(double));
matGetDbl( "time", num_time_steps, 1,scr);
for (i=0;i<num_time_steps;i++){
ex_put_time(exo_file,i+1,&scr[i]);
}
free(scr);
}
/* global variables */
if (num_global_vars > 0 ){
int max_name_length = ex_inquire_int(exo_file, EX_INQ_DB_MAX_USED_NAME_LENGTH);
char *str = (char *) calloc(num_global_vars * (max_name_length+1), sizeof(char));
matGetStr("gnames",str);
str2 = (char **) calloc(num_global_vars,sizeof(char*));
curr = strtok(str,"\n");
for(i=0;i<num_global_vars;i++){
str2[i]=curr;
curr = strtok(NULL,"\n");
}
ex_put_variable_names(exo_file, EX_GLOBAL, num_global_vars, str2);
free(str);
free(str2);
{
double * global_var_vals;
double * temp;
global_var_vals = (double *) calloc(num_global_vars*num_time_steps,sizeof(double));
temp = (double *) calloc(num_time_steps,sizeof(double));
for (j=0;j<num_global_vars;j++) {
char name[32];
sprintf(name,"gvar%02d",j+1);
matGetDbl(name,num_time_steps,1,temp);
for (i=0; i < num_time_steps; i++) {
global_var_vals[num_global_vars*i+j]=temp[i];
}
}
for (i=0; i<num_time_steps; i++) {
size_t offset = num_global_vars * i;
ex_put_var(exo_file,i+1,EX_GLOBAL,1,0,num_global_vars,&global_var_vals[offset]);
}
free(temp);
free(global_var_vals);
}
}
/* nodal variables */ /* section by dtg */
if (num_nodal_vars > 0){
int max_name_length = ex_inquire_int(exo_file, EX_INQ_DB_MAX_USED_NAME_LENGTH);
char *str = (char *) calloc(num_nodal_vars * (max_name_length+1), sizeof(char));
matGetStr("nnames",str);
str2 = (char **) calloc(num_nodal_vars,sizeof(char*));
curr = strtok(str,"\n");
for(i=0;i<num_nodal_vars;i++){
str2[i]=curr;
curr = strtok(NULL,"\n");
}
ex_put_variable_names(exo_file, EX_NODAL, num_nodal_vars, str2);
free(str);
free(str2);
{
double * nodal_var_vals;
for (i=0;i<num_nodal_vars;i++) {
char name[32];
nodal_var_vals = (double *) calloc(num_nodes*num_time_steps,sizeof(double));
sprintf(name,"nvar%02d",i+1);
matGetDbl(name,num_nodes,num_time_steps,nodal_var_vals);
for (j=0;j<num_time_steps;j++) {
ex_put_var(exo_file,j+1,EX_NODAL,i+1,num_nodes,1,nodal_var_vals+num_nodes*j);
}
free(nodal_var_vals);
}
}
}
/* elemental variables */ /* section by dtg */
if (num_element_vars > 0){
int max_name_length = ex_inquire_int(exo_file, EX_INQ_DB_MAX_USED_NAME_LENGTH);
char *str = (char *) calloc(num_element_vars * (max_name_length+1), sizeof(char));
matGetStr("enames",str);
str2 = (char **) calloc(num_element_vars,sizeof(char*));
curr = strtok(str,"\n");
for(i=0;i<num_element_vars;i++){
str2[i]=curr;
curr = strtok(NULL,"\n");
}
ex_put_variable_names(exo_file, EX_ELEM_BLOCK, num_element_vars, str2);
free(str);
free(str2);
{
double * element_var_vals;
for (i=0;i<num_element_vars;i++) {
char name[32];
element_var_vals = (double *) calloc(num_elements*num_time_steps,sizeof(double));
sprintf(name,"evar%02d",i+1);
matGetDbl(name,num_elements,num_time_steps,element_var_vals);
n=0;
for (j=0;j<num_time_steps;j++) {
for (k=0;k<num_blocks;k++) {
ex_put_var(exo_file,j+1,EX_ELEM_BLOCK, i+1,ids[k],num_elem_in_block[k],element_var_vals+n);
n=n+num_elem_in_block[k];
}
}
free(element_var_vals);
}
}
}
free(ids);
/* node and element number maps */
ids = (int *) calloc (num_nodes,sizeof(int));
if ( !matGetInt("node_num_map",num_nodes,1,ids)){
ex_put_node_num_map(exo_file,ids);
}
free(ids);
ids = (int *) calloc (num_elements,sizeof(int));
if ( !matGetInt("elem_num_map",num_elements,1,ids)){
ex_put_elem_num_map(exo_file,ids);
}
free(ids);
free(num_elem_in_block);
/* close exo file */
ex_close(exo_file);
/* close mat file */
Mat_Close(mat_file);
/* */
fprintf(stderr,"done.\n");
/* exit status */
add_to_log("mat2exo", 0);
return(0);
}
int
main (int argc, char *argv[])
{
char *prog_name = "matdump";
int i, c, err = EXIT_SUCCESS;
mat_t *mat;
matvar_t *matvar;
int version[3];
Mat_GetLibraryVersion(version, version+1, version+2);
if ( MATIO_MAJOR_VERSION != version[0] ||
MATIO_MINOR_VERSION != version[1] ||
MATIO_RELEASE_LEVEL != version[2] ) {
fprintf(stderr,"matio version in header does not match runtime "
"version\n");
return EXIT_FAILURE;
}
Mat_LogInitFunc(prog_name,default_printf_func);
printfunc = print_default;
while ((c = getopt_long(argc,argv,optstring,options,NULL)) != EOF) {
switch (c) {
case 'd':
printdata = 1;
Mat_VerbMessage(1,"Printing data\n");
break;
case 'f':
if ( NULL != optarg && !strcmp(optarg,"whos") ) {
printfunc = print_whos;
break;
}
Mat_Warning("%s is not a recognized output format. "
"Using default\n", optarg);
break;
case 'h':
human_readable = 1;
break;
case 'v':
Mat_SetVerbose(1,0);
break;
case 'H':
Mat_Help(helpstr);
exit(EXIT_SUCCESS);
case 'V':
printf("%s %s\nWritten by Christopher Hulbert\n\n"
"Copyright(C) 2006-2013 Christopher C. Hulbert\n",
prog_name,MATIO_VERSION_STR);
exit(EXIT_SUCCESS);
default:
printf("%c not a valid option\n", c);
break;
}
}
if ( (argc-optind) < 1 )
Mat_Error("Must specify at least one argument");
mat = Mat_Open( argv[optind],MAT_ACC_RDONLY );
if ( NULL == mat ) {
Mat_Error("Error opening %s\n", argv[optind]);
return EXIT_FAILURE;
}
optind++;
if ( optind < argc ) {
/* variables specified on the command line */
for ( i = optind; i < argc; i++ ) {
char *next_tok_pos, next_tok = 0;
next_tok_pos = get_next_token(argv[i]);
if ( next_tok_pos != argv[i] ) {
next_tok = *next_tok_pos;
*next_tok_pos = '\0';
}
matvar = Mat_VarReadInfo(mat,argv[i]);
if ( matvar ) {
if ( printdata ) {
if ( next_tok == '\0' ) {
/* No indexing tokens found, so read all of the data */
Mat_VarReadDataAll(mat,matvar);
} else {
*next_tok_pos = next_tok;
read_selected_data(mat,matvar,next_tok_pos);
}
}
(*printfunc)(matvar);
Mat_VarFree(matvar);
matvar = NULL;
} else {
Mat_Warning("Couldn't find variable %s in the MAT file",
argv[i]);
}
} /* for ( i = optind; i < argc; i++ ) */
} else {
/* print all variables */
if ( printdata ) {
while ( (matvar = Mat_VarReadNext(mat)) != NULL ) {
(*printfunc)(matvar);
Mat_VarFree(matvar);
matvar = NULL;
}
} else {
while ( (matvar = Mat_VarReadNextInfo(mat)) != NULL ) {
(*printfunc)(matvar);
Mat_VarFree(matvar);
matvar = NULL;
}
}
}
Mat_Close(mat);
Mat_LogClose();
return err;
}
int main(int argn, char **argc){
if(argn != 3){
printf("usage: convert infile.bin outfile.mat\n");
exit(0);
} else {
FILE* in = fopen(argc[1], "r");
if(!in) {
printf("could not open %s\n", argc[1]);
exit(0);
}
mat_t *mat;
mat = Mat_Create(argc[2],NULL);
if(!mat){
printf("could not open for writing %s\n", argc[2]);
exit(0);
}
//this is (for now) a two-stage process:
//have to scan through the file,
//determine what's there, allocate memory appropritately,
//then fill those structures up and write *that* out.
unsigned int u;
unsigned int pos = 0;
unsigned int rxpackets = 0;
unsigned int txpackets = 0;
unsigned int msgpackets = 0;
bool done = false;
while(!done){
fread((void*)&u,4,1,in);
if(ferror(in) || feof(in)) done = true;
else {
if(u == 0xdecafbad){
fread((void*)&u,4,1,in);
unsigned int siz = u & 0xffff;
//printf("u 0x%x\n",u);
rxpackets += (siz-4)/(32+4);
fseek(in,siz+8, SEEK_CUR);
pos += 16+siz;
}else if(u == 0xc0edfad0){
fread((void*)&u,4,1,in);
unsigned int siz = u & 0xffff;
//printf("u 0x%x\n",u);
txpackets++;
fseek(in,siz+8, SEEK_CUR);
pos += 16+siz;
}else if(u == 0xb00a5c11){
fread((void*)&u,4,1,in);
unsigned int siz = u & 0xffff;
//printf("u 0x%x\n",u);
msgpackets += 1;
fseek(in,siz+8, SEEK_CUR);
pos += 16+siz;
} else {
printf("magic number seems off, is 0x%x, %d bytes, %d packets\n",
u,pos,rxpackets);
exit(0);
}
if(ferror(in) || feof(in)) done = true;
}
}
printf("total %d rxpackets, %d txpackets, %d messages\n",
rxpackets, txpackets, msgpackets);
fseek(in,0, SEEK_SET);
//okay, allocate appropriate data structs:
// time (double), analog(i8), channel (i8),
// spike_time (double), spikes(i32)
double* time;
mat_uint32_t* mstimer;
mat_int8_t* analog;
mat_int8_t* channel;
mat_uint32_t* spike_ts;
mat_int8_t* spike_ch;
mat_int8_t* spike_unit;
// store timestamp (in samples), rx time (not necessarily accurate) - one per pkt
// store channel # and sample
// store channel & timestamp for spikes.
// just ignore dropped packets for now.
time = (double*)malloc(rxpackets * sizeof(double));
if(!time){ printf("could not allocate time variable."); exit(0);}
mstimer = (mat_uint32_t*)malloc(rxpackets * sizeof(int) );
if(!mstimer){ printf("could not allocate mstimer variable."); exit(0);}
analog = (mat_int8_t*)malloc(rxpackets * 24 );
if(!analog){ printf("could not allocate analog variable."); exit(0);}
channel = (mat_int8_t*)malloc(rxpackets * 24 );
if(!channel){ printf("could not allocate channel variable."); exit(0);}
spike_ts = (mat_uint32_t*)malloc(rxpackets * sizeof(int)*32);
if(!spike_ts){ printf("could not allocate spike_ts variable."); exit(0);}
spike_ch = (mat_int8_t*)malloc(rxpackets * 32);
if(!spike_ch){ printf("could not allocate spike_ch variable."); exit(0);}
spike_unit = (mat_int8_t*)malloc(rxpackets * 32);
if(!spike_unit){ printf("could not allocate spike_unit variable."); exit(0);}
//also need to inspect the messages, to see exactly when the channels changed.
rxpackets = 0;
int tp = 0; // packet position (index time, aka timestamp)
int sp = 0; // spike position (index spike variables)
char msgs[16][128]; //use this to save messages ; appy them when their echo appears.
for(int i=0; i<16*128; i++){
msgs[0][i] = 0; //yes, you can do that in c!
}
int chans[4] = {0,32,64,96};
done = false;
while(!done){
fread((void*)&u,4,1,in);
if(ferror(in) || feof(in)) done = true;
else {
if(u == 0xdecafbad){
fread((void*)&u,4,1,in);
unsigned int siz = u & 0xffff;
int npak = (siz-4)/(4+32);
//first 4 is for dropped packet count
//second 4 is for 4 byte bridge milisecond counter
//printf("npak %d siz %d\n",npak,siz);
double rxtime = 0.0;
unsigned int dropped = 0;
fread((void*)&rxtime,8,1,in); //rx time in seconds.
fread((void*)&dropped,4,1,in);
int channels[32]; char match[32];
for(int i=0;i<npak; i++){
packet p;
fread((void*)&p,sizeof(p),1,in);
if(ferror(in) || feof(in)) done = true;
else{
/*int headecho = ((p.flag) >> 4) & 0xf;
//check to see if we can apply the command that was echoed.
char m = msgs[headecho][0];
if(m >= 'A' && m <= 'A' + 15){
printf("applying %s\n", msgs[headecho]);
msgs[headecho][0] = 0;
}*/
time[tp] = rxtime + (double)i * 6.0 / 31250.0;
mstimer[tp] = p.ms;
for(int j=0; j<6; j++){
for(int k=0; k<4; k++){
char samp = p.data[j*4+k];
analog[tp*24+j*4+k] = samp;
channel[tp*24+j*4+k] = chans[k];
}
}
decodePacket(&p, channels, match);
for(int j=0; j<32; j++){
if(match[j]){
spike_ts[sp] = tp;
spike_ch[sp] = channel[j];
spike_unit[sp] = match[j];
sp++;
}
}
tp++;
}
}
pos += 16+siz;
} else if( u == 0xc0edfad0){
//ignore tx packets (for now?)
fread((void*)&u,4,1,in);
unsigned int siz = u & 0xffff;
//printf("u 0x%x\n",u);
txpackets += (siz)/32;
fseek(in,siz+8, SEEK_CUR);
pos += 16+siz;
} else if(u == 0xb00a5c11){
fread((void*)&u,4,1,in);
unsigned int siz = u & 0xffff;
//printf("u 0x%x\n",u);
double rxtime = 0.0;
fread((void*)&rxtime,8,1,in);
char buf[128];
fread((void*)buf,siz,1,in);
buf[siz] = 0;
//really need to wait for the echo here.
//bummish.
printf("message: %s\n", buf);
//first char: A-P (0-15, corresponds to echo); second space
char* b = buf; b+=2;
if(strncmp(b, "chan", 4) == 0){
int ii = b[5] - 'A';
if(ii >= 0 && ii < 4){
b += 7;
chans[ii] = atoi(b);
//printf(" chan %d changed to %d\n", ii, chans[ii]);
}
}
pos += 16+siz;
} else {
printf("magic number seems off, is 0x%x, %d bytes\n",
u,pos);
exit(0);
}
}
}
printf("finished reading in data file, now writing matlab file.\n");
matvar_t *matvar;
matvar = Mat_VarCreate("time",MAT_C_DOUBLE,MAT_T_DOUBLE,
1,&tp,time,0);
Mat_VarWrite( mat, matvar, 0 );
Mat_VarFree(matvar);
free(time); //I wish I had more.
matvar = Mat_VarCreate("mstimer",MAT_C_UINT32,MAT_T_UINT32,
1,&tp,mstimer,0);
Mat_VarWrite( mat, matvar, 0 );
Mat_VarFree(matvar);
free(mstimer);
int m = tp * 24;
matvar = Mat_VarCreate("analog",MAT_C_INT8,MAT_T_INT8,
1,&m,analog,0);
Mat_VarWrite( mat, matvar, 0 );
Mat_VarFree(matvar);
free(analog);
matvar = Mat_VarCreate("channel",MAT_C_INT8,MAT_T_INT8,
1,&m,channel,0);
Mat_VarWrite( mat, matvar, 0 );
Mat_VarFree(matvar);
free(channel);
matvar = Mat_VarCreate("spike_ts",MAT_C_UINT32,MAT_T_UINT32,
1,&sp,spike_ts,0);
Mat_VarWrite( mat, matvar, 0 );
Mat_VarFree(matvar);
free(spike_ts);
matvar = Mat_VarCreate("spike_ch",MAT_C_UINT32,MAT_T_UINT32,
1,&sp,spike_ch,0);
Mat_VarWrite( mat, matvar, 0 );
Mat_VarFree(matvar);
free(spike_ch);
matvar = Mat_VarCreate("spike_unit",MAT_C_UINT32,MAT_T_UINT32,
1,&sp,spike_unit,0);
Mat_VarWrite( mat, matvar, 0 );
Mat_VarFree(matvar);
free(spike_unit);
Mat_Close(mat);
fclose(in);
}
}
int main (int argc, char *argv[])
{
char
*str,**str2,*(*qa_records)[4],*line, *oname, *dot, *filename;
const char* ext=EXT;
int
i,j,k,n,n1,n2,cpu_word_size,io_word_size,exo_file,err,
num_axes,num_nodes,num_elements,num_blocks,
num_side_sets,num_node_sets,num_time_steps,
num_qa_lines,num_info_lines,num_global_vars,
num_nodal_vars,num_element_vars,num_nodeset_vars, num_sideset_vars,
*ids,*iscr,*num_elem_in_block,*junk,
*elem_list,*side_list,
*nsssides,*nssdfac,
*nnsnodes,*nnsdfac,
nstr2, has_ss_dfac;
float
exo_version;
double
*scr,*x,*y,*z;
oname=0;
/* process arguments */
for (j=1; j< argc; j++){
if ( strcmp(argv[j],"-t")==0){ /* write text file (*.m) */
del_arg(&argc,argv,j);
textfile=1;
j--;
continue;
}
if ( strcmp(argv[j],"-o")==0){ /* specify output file name */
del_arg(&argc,argv,j);
if ( argv[j] ){
oname=(char*)calloc(strlen(argv[j])+10,sizeof(char));
strcpy(oname,argv[j]);
del_arg(&argc,argv,j);
printf("output file: %s\n",oname);
}
else {
fprintf(stderr,"Invalid output file specification.\n");
return 2;
}
j--;
continue;
}
}
/* QA Info */
printf("%s: %s, %s\n", qainfo[0], qainfo[2], qainfo[1]);
/* usage message*/
if(argc != 2){
printf("%s [options] exodus_file_name.\n",argv[0]);
printf(" the exodus_file_name is required (exodusII only).\n");
printf(" Options:\n");
printf(" -t write a text (.m) file rather than a binary .mat\n");
printf(" -o output file name (rather than auto generate)\n");
printf(" ** note **\n");
printf("Binary files are written by default on all platforms with");
printf(" available libraries.\n");
exit(1);
}
/* open output file */
if ( textfile )
ext=".m";
if ( !oname ){
filename = (char*)malloc( strlen(argv[1])+10);
strcpy(filename,argv[1]);
dot=strrchr(filename,'.');
if ( dot ) *dot=0;
strcat(filename,ext);
}
else {
filename=oname;
}
if ( textfile ){
m_file = fopen(filename,"w");
if (!m_file ){
fprintf(stderr,"Unable to open %s\n",filename);
exit(1);
}
}
else {
mat_file = Mat_CreateVer(filename, NULL, MAT_FT_MAT5);
if (mat_file == NULL) {
fprintf(stderr,"Unable to create matlab file %s\n",filename);
exit(1);
}
}
/* word sizes */
cpu_word_size=sizeof(double);
io_word_size=0;
/* open exodus file */
exo_file=ex_open(argv[1],EX_READ,&cpu_word_size,&io_word_size,&exo_version);
if (exo_file < 0){
printf("error opening %s\n",argv[1]);
exit(1);
}
/* print */
fprintf(stderr,"translating %s to %s ...\n",argv[1],filename);
/* read database paramters */
line=(char *) calloc ((MAX_LINE_LENGTH+1),sizeof(char));
err = ex_get_init(exo_file,line,
&num_axes,&num_nodes,&num_elements,&num_blocks,
&num_node_sets,&num_side_sets);
num_qa_lines = ex_inquire_int(exo_file,EX_INQ_QA);
num_info_lines = ex_inquire_int(exo_file,EX_INQ_INFO);
num_time_steps = ex_inquire_int(exo_file,EX_INQ_TIME);
err=ex_get_variable_param(exo_file,EX_GLOBAL,&num_global_vars);
err=ex_get_variable_param(exo_file,EX_NODAL,&num_nodal_vars);
err=ex_get_variable_param(exo_file,EX_ELEM_BLOCK,&num_element_vars);
err=ex_get_variable_param(exo_file,EX_NODE_SET,&num_nodeset_vars);
err=ex_get_variable_param(exo_file,EX_SIDE_SET,&num_sideset_vars);
/* export paramters */
PutInt("naxes", 1, 1,&num_axes);
PutInt("nnodes", 1, 1,&num_nodes);
PutInt("nelems", 1, 1,&num_elements);
PutInt("nblks", 1, 1,&num_blocks);
PutInt("nnsets", 1, 1,&num_node_sets);
PutInt("nssets", 1, 1,&num_side_sets);
PutInt("nsteps", 1, 1,&num_time_steps);
PutInt("ngvars", 1, 1,&num_global_vars);
PutInt("nnvars", 1, 1,&num_nodal_vars);
PutInt("nevars", 1, 1,&num_element_vars);
PutInt("nnsvars", 1, 1,&num_nodeset_vars);
PutInt("nssvars", 1, 1,&num_sideset_vars);
/* allocate -char- scratch space*/
n = num_info_lines;
n = (n > num_global_vars) ? n : num_global_vars;
n = (n > num_nodal_vars) ? n : num_nodal_vars;
n = (n > num_element_vars) ? n : num_element_vars;
n = (n > num_blocks) ? n : num_blocks;
nstr2 = n;
str2= (char **) calloc (n,sizeof(char *));
for (i=0;i<nstr2;i++)
str2[i]=(char *) calloc ((MAX_LINE_LENGTH+1),sizeof(char));
str= (char *) calloc ((MAX_LINE_LENGTH+1)*n,sizeof(char));
/* title */
PutStr("Title",line);
#if 0
/* QA records */
if (num_qa_lines > 0 ){
qa_records =(char *(*)[4]) calloc (num_qa_lines*4,sizeof(char **));
for (i=0;i<num_qa_lines;i++)
for (j=0;j<4;j++)
qa_records[i][j]=(char *) calloc ((MAX_STR_LENGTH+1),sizeof(char));
err=ex_get_qa(exo_file,qa_records);
str[0]='\0';
for (i=0;i<num_qa_lines;i++){
for (j=0;j<4;j++)
sprintf(str+strlen(str),"%s ",qa_records[i][j]);
strcat(str,"\n");
}
for (i=0;i<num_qa_lines;i++){
for (j=0;j<4;j++)
free(qa_records[i][j]);
}
free(qa_records);
}
/* information records */
if (num_info_lines > 0 ){
err = ex_get_info(exo_file,str2);
str[0]='\0';
for (i=0;i<num_info_lines;i++)
sprintf(str+strlen(str),"%s\n",str2[i]);
PutStr("info",str);
str[0]='\0';
for (i=0;i<num_info_lines;i++)
if (strncmp(str2[i],"cavi",4)==0)
sprintf(str+strlen(str),"%s\n",str2[i]);
PutStr("cvxp",str);
}
#endif
/* nodal coordinates */
x = (double *) calloc(num_nodes,sizeof(double));
y = (double *) calloc(num_nodes,sizeof(double));
if (num_axes == 3)
z = (double *) calloc(num_nodes,sizeof(double));
else
z = NULL;
err = ex_get_coord(exo_file,x,y,z);
PutDbl("x0", num_nodes, 1, x);
PutDbl("y0", num_nodes, 1, y);
free(x);
free(y);
if (num_axes == 3){
PutDbl("z0",num_nodes,1, z);
free(z);
}
/* side sets */
if(num_side_sets > 0){
ids=(int *) calloc(num_side_sets,sizeof(int));
err = ex_get_ids(exo_file,EX_SIDE_SET,ids);
PutInt( "ssids",num_side_sets, 1,ids);
nsssides = (int *) calloc(num_side_sets,sizeof(int)); /*dgriffi */
nssdfac = (int *) calloc(num_side_sets,sizeof(int)); /*dgriffi */
for (i=0;i<num_side_sets;i++){
err = ex_get_set_param(exo_file,EX_SIDE_SET, ids[i],&n1,&n2);
nsssides[i]=n1; /* dgriffi */
nssdfac[i]=n2; /* dgriffi */
/*
* the following provision is from Version 1.6 when there are no
* distribution factors in exodus file
*/
has_ss_dfac = (n2 != 0);
if(n2==0 || n1==n2){
printf(" WARNING: Exodus II file does not contain distribution factors.\n");
/* n1=number of faces, n2=number of df */
/* using distribution factors to determine number of nodes in the sideset
causes a lot grief since some codes do not output distribution factors
if they are all equal to 1. mkbhard: I am using the function call below
to figure out the total number of nodes in this sideset. Some redundancy
exists, but it works for now */
junk = (int*) calloc(n1,sizeof(int));
err = ex_get_side_set_node_count(exo_file,ids[i],junk);
n2=0; /* n2 will be equal to the total number of nodes in the sideset */
for (j=0;j<n1;j++) n2+=junk[j];
free(junk);
}
iscr = (int *) calloc(n1+n2,sizeof(int));
err = ex_get_side_set_node_list(exo_file,ids[i],iscr,iscr+n1);
/* number-of-nodes-per-side list */
sprintf(str,"ssnum%02d",i+1);
PutInt(str,n1,1,iscr);
/* nodes list */
sprintf(str,"ssnod%02d",i+1);
PutInt(str,n2,1,iscr+n1);
free(iscr);
/* distribution-factors list */
scr = (double *) calloc (n2,sizeof(double));
if (has_ss_dfac) {
ex_get_side_set_dist_fact(exo_file,ids[i],scr);
} else {
for (j=0; j<n2; j++) {
scr[j] = 1.0;
}
}
sprintf(str,"ssfac%02d",i+1);
PutDbl(str,n2,1,scr);
free(scr);
/* element and side list for side sets (dgriffi) */
elem_list = (int *) calloc(n1, sizeof(int));
side_list = (int *) calloc(n1, sizeof(int));
err = ex_get_set(exo_file,EX_SIDE_SET,ids[i],elem_list,side_list);
sprintf(str,"ssside%02d",i+1);
PutInt(str,n1,1,side_list);
sprintf(str,"sselem%02d",i+1);
PutInt(str,n1,1,elem_list);
free(elem_list);
free(side_list);
}
/* Store # sides and # dis. factors per side set (dgriffi) */
PutInt("nsssides",num_side_sets,1,nsssides);
PutInt("nssdfac",num_side_sets,1,nssdfac);
free(ids);
free(nsssides);
free(nssdfac);
}
/* node sets (section by dgriffi) */
if(num_node_sets > 0){
ids=(int *) calloc(num_node_sets,sizeof(int));
err = ex_get_ids(exo_file,EX_NODE_SET, ids);
PutInt( "nsids",num_node_sets, 1,ids);
nnsnodes = (int *) calloc(num_node_sets,sizeof(int));
nnsdfac = (int *) calloc(num_node_sets,sizeof(int));
for (i=0;i<num_node_sets;i++){
err = ex_get_set_param(exo_file,EX_NODE_SET,ids[i],&n1,&n2);
iscr = (int *) calloc(n1,sizeof(int));
err = ex_get_node_set(exo_file,ids[i],iscr);
/* nodes list */
sprintf(str,"nsnod%02d",i+1);
PutInt(str,n1,1,iscr);
free(iscr);
/* distribution-factors list */
scr = (double *) calloc (n2,sizeof(double));
ex_get_node_set_dist_fact(exo_file,ids[i],scr);
sprintf(str,"nsfac%02d",i+1);
PutDbl(str,n2,1,scr);
free(scr);
nnsnodes[i]=n1;
nnsdfac[i]=n2;
}
/* Store # nodes and # dis. factors per node set */
PutInt("nnsnodes",num_node_sets,1,nnsnodes);
PutInt("nnsdfac",num_node_sets,1,nnsdfac);
free(ids);
free(nnsdfac);
free(nnsnodes);
}
/* element blocks */
ids=(int *) calloc(num_blocks,sizeof(int));
num_elem_in_block=(int *) calloc(num_blocks,sizeof(int));
err = ex_get_ids(exo_file,EX_ELEM_BLOCK,ids);
PutInt( "blkids",num_blocks, 1,ids);
for (i=0;i<num_blocks;i++) {
err = ex_get_elem_block(exo_file,ids[i],str2[i],&n,&n1,&n2);
num_elem_in_block[i]=n;
iscr = (int *) calloc(n*n1,sizeof(int));
err = ex_get_conn(exo_file,EX_ELEM_BLOCK,ids[i],iscr, NULL, NULL);
sprintf(str,"blk%02d",i+1);
PutInt(str,n1,n,iscr);
free(iscr);
}
str[0]='\0';
for (i=0;i<num_blocks;i++)
sprintf(str+strlen(str),"%s\n",str2[i]);
PutStr("blknames",str);
/* time values */
if (num_time_steps > 0 ) {
scr = (double *) calloc (num_time_steps,sizeof(double));
err= ex_get_all_times (exo_file,scr);
PutDbl( "time", num_time_steps, 1,scr);
free(scr);
}
/* global variables */
if (num_global_vars > 0 ) {
err = ex_get_variable_names(exo_file,EX_GLOBAL,num_global_vars,str2);
str[0]='\0';
for (i=0;i<num_global_vars;i++)
sprintf(str+strlen(str),"%s\n",str2[i]);
PutStr("gnames",str);
scr = (double *) calloc (num_time_steps,sizeof(double));
for (i=0;i<num_global_vars;i++){
sprintf(str,"gvar%02d",i+1);
err=ex_get_glob_var_time(exo_file,i+1,1,num_time_steps,scr);
PutDbl(str,num_time_steps,1,scr);
}
free(scr);
}
/* nodal variables */
if (num_nodal_vars > 0 ) {
err = ex_get_variable_names(exo_file,EX_NODAL,num_nodal_vars,str2);
str[0]='\0';
for (i=0;i<num_nodal_vars;i++)
sprintf(str+strlen(str),"%s\n",str2[i]);
PutStr("nnames",str);
scr = (double *) calloc (num_nodes*num_time_steps,sizeof(double));
for (i=0;i<num_nodal_vars;i++){
sprintf(str,"nvar%02d",i+1);
for (j=0;j<num_time_steps;j++)
err=ex_get_nodal_var(exo_file,j+1,i+1,num_nodes,
scr+num_nodes*j);
PutDbl(str,num_nodes,num_time_steps,scr);
}
free(scr);
}
/* element variables */
if (num_element_vars > 0 ) {
err = ex_get_variable_names(exo_file,EX_ELEM_BLOCK,num_element_vars,str2);
str[0]='\0';
for (i=0;i<num_element_vars;i++)
sprintf(str+strlen(str),"%s\n",str2[i]);
PutStr("enames",str);
/* truth table */
iscr = (int *) calloc(num_element_vars*num_blocks, sizeof(int));
ex_get_elem_var_tab(exo_file,num_blocks,num_element_vars,iscr);
for (i=0;i<num_element_vars;i++){
scr = (double *) calloc (num_elements*num_time_steps,sizeof(double));
n=0;
sprintf(str,"evar%02d",i+1);
for (j=0;j<num_time_steps;j++){
for (k=0;k<num_blocks;k++){
if(iscr[num_element_vars*k+i]==1)
ex_get_elem_var(exo_file,j+1,i+1,ids[k],num_elem_in_block[k],scr+n);
n=n+num_elem_in_block[k];
}
}
PutDbl(str,num_elements,num_time_steps,scr);
free(scr);
}
free(iscr);
}
free(num_elem_in_block);
free(ids);
/* node and element number maps */
ex_opts(0); /* turn off error reporting. It is not an error to have no map*/
ids = (int *)malloc(num_nodes*sizeof(int));
err = ex_get_node_num_map(exo_file,ids);
if ( err==0 ){
PutInt("node_num_map",num_nodes,1,ids);
}
free(ids);
ids = (int *)malloc(num_elements*sizeof(int));
err = ex_get_elem_num_map(exo_file,ids);
if ( err==0 ){
PutInt("elem_num_map",num_elements,1,ids);
}
free(ids);
/* close exo file */
ex_close(exo_file);
/* close mat file */
if ( textfile )
fclose(m_file);
else
Mat_Close(mat_file);
/* */
fprintf(stderr,"done.\n");
free(filename);
free(line);
free(str);
for (i=0;i<nstr2;i++)
free(str2[i]);
free(str2);
/* exit status */
add_to_log("exo2mat", 0);
return(0);
}
// load a .mat matlab matrix
// will load the first matrix (sparse or dense) in the file
// returns 0 on success
static
int read_mat(char const *const filename,
matrix_t *const A) {
#ifndef HAVE_MATIO
return 1;
#else
const int LOCAL_DEBUG = 0;
mat_t* matfp;
matfp = Mat_Open(filename, MAT_ACC_RDONLY);
if(matfp == NULL)
return 1; // failed to open file
matvar_t* t;
int more_data = 1;
while (more_data) {
t = Mat_VarReadNextInfo(matfp);
if(t == NULL) {
return 2; // no suitable variable found
}
// TODO decide if this is the one: if(t->
if(1) {
more_data = 0;
}
else { // keep going
Mat_VarFree(t);
t = NULL;
}
}
{ // load the selected variable, including data
Mat_Rewind(matfp);
matvar_t* tt = Mat_VarRead(matfp, t->name);
Mat_VarFree(t);
t = tt;
if(LOCAL_DEBUG) Mat_VarPrint(tt, 1);
}
// debug info
if(LOCAL_DEBUG && t->name != NULL)
printf("%s: loaded variable %s\n", filename, t->name);
// checks and data handling
int ret = 0;
if(t->rank > 2 || t->rank <= 0) { // number of dimensions
ret = 2;
}
else if(t->data_type != MAT_T_DOUBLE) {
if(LOCAL_DEBUG) printf("data_type=%d\n",t->data_type);
ret = 3;
}
else if(t->isComplex) {
ret = 10; // TODO can't handle complex matrices yet
}
else if(t->isLogical) {
ret = 11; // TODO can't handle logicals yet
}
else {
if(t->rank == 1) {
A->m = t->dims[0]; // rows
A->n = 1; // cols
}
else {
A->m = t->dims[0]; // rows
A->n = t->dims[1]; // cols
}
A->sym = SM_UNSYMMETRIC;
//if(t->data_type == MAT_T_DOUBLE) {
A->data_type = REAL_DOUBLE;
//} // TODO complex, single precision, various sized integers
if(t->class_type == MAT_C_SPARSE) { // t.data = sparse_t in CSC format
// Note that Matlab will save('-v4'...) a sparse matrix
// to version 4 format without complaint but it appears
// to be gibberish as far as MatIO is concerned
sparse_t* st = t->data;
A->nz = st->ndata; //st->nzmax has the actual size of the allocated st->data
A->format = SM_CSC;
// transfer the data pointer into our strucut
// TODO check for negative values in ir/jc before throwing away their signs
A->ii = (unsigned int*) st->ir;
st->ir = NULL;
A->jj = (unsigned int*) st->jc;
st->jc = NULL;
A->dd = st->data;
st->data = NULL;
}
else if(t->class_type == MAT_C_DOUBLE) {
A->nz = A->m * A->n;
A->format = DCOL;
// transfer the data pointer into our struct
A->dd = t->data;
t->data = NULL;
}
else {
ret = 4; // unknown class of data structure
}
}
// DEBUG
if(LOCAL_DEBUG && validate_matrix(A) != 0) {
ret = 50;
fprintf(stderr, "problem loading .mat matrix file\n");
printf_matrix(" ", A);
}
// sanity checks
// t.dims[] is don't-care
// t.isGlobal is don't-care
Mat_Close(matfp);
Mat_VarFree(t);
return ret; // success?
#endif
}
void SimpleVector<Scalar>::export_to_file(const char *filename, const char *var_name, MatrixExportFormat fmt, char* number_format)
{
if (!v)
throw Exceptions::MethodNotOverridenException("Vector<Scalar>::export_to_file");
switch (fmt)
{
case EXPORT_FORMAT_MATRIX_MARKET:
{
FILE* file = fopen(filename, "w");
if (!file)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
if (Hermes::Helpers::TypeIsReal<Scalar>::value)
fprintf(file, "%%%%MatrixMarket matrix coordinate real general\n");
else
fprintf(file, "%%%%MatrixMarket matrix coordinate complex general\n");
fprintf(file, "%d 1 %d\n", this->size, this->size);
for (unsigned int j = 0; j < this->size; j++)
{
Hermes::Helpers::fprint_coordinate_num(file, j + 1, 1, v[j], number_format);
fprintf(file, "\n");
}
fclose(file);
}
break;
case EXPORT_FORMAT_MATLAB_MATIO:
{
#ifdef WITH_MATIO
size_t dims[2];
dims[0] = this->size;
dims[1] = 1;
mat_t *mat = Mat_CreateVer(filename, "", MAT_FT_MAT5);
matvar_t *matvar;
// For complex.
double* v_re = nullptr;
double* v_im = nullptr;
void* data;
if (Hermes::Helpers::TypeIsReal<Scalar>::value)
{
data = v;
matvar = Mat_VarCreate(var_name, MAT_C_DOUBLE, MAT_T_DOUBLE, 2, dims, data, MAT_F_DONT_COPY_DATA);
}
else
{
v_re = malloc_with_check<SimpleVector<Scalar>, double>(this->size, this);
v_im = malloc_with_check<SimpleVector<Scalar>, double>(this->size, this);
struct mat_complex_split_t z = { v_re, v_im };
for (int i = 0; i < this->size; i++)
{
v_re[i] = ((std::complex<double>)(this->v[i])).real();
v_im[i] = ((std::complex<double>)(this->v[i])).imag();
data = &z;
}
matvar = Mat_VarCreate(var_name, MAT_C_DOUBLE, MAT_T_DOUBLE, 2, dims, data, MAT_F_DONT_COPY_DATA | MAT_F_COMPLEX);
}
if (matvar)
{
Mat_VarWrite(mat, matvar, MAT_COMPRESSION_ZLIB);
Mat_VarFree(matvar);
}
free_with_check(v_re);
free_with_check(v_im);
Mat_Close(mat);
if (!matvar)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
#else
throw Exceptions::Exception("MATIO not included.");
#endif
}
break;
case EXPORT_FORMAT_PLAIN_ASCII:
case EXPORT_FORMAT_MATLAB_SIMPLE:
{
FILE* file = fopen(filename, "w");
if (!file)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
for (unsigned int i = 0; i < this->size; i++)
{
Hermes::Helpers::fprint_num(file, v[i], number_format);
fprintf(file, "\n");
}
fclose(file);
}
break;
#ifdef WITH_BSON
case EXPORT_FORMAT_BSON:
{
// Init bson
bson bw;
bson_init(&bw);
// Matrix size.
bson_append_int(&bw, "size", this->size);
bson_append_start_array(&bw, "v");
for (unsigned int i = 0; i < this->size; i++)
bson_append_double(&bw, "v_i", real(this->v[i]));
bson_append_finish_array(&bw);
if (!Hermes::Helpers::TypeIsReal<Scalar>::value)
{
bson_append_start_array(&bw, "v-imag");
for (unsigned int i = 0; i < this->size; i++)
bson_append_double(&bw, "v_i", imag(this->v[i]));
bson_append_finish_array(&bw);
}
// Done.
bson_finish(&bw);
// Write to disk.
FILE *fpw;
fpw = fopen(filename, "wb");
const char *dataw = (const char *)bson_data(&bw);
fwrite(dataw, bson_size(&bw), 1, fpw);
fclose(fpw);
bson_destroy(&bw);
}
#endif
}
}
void SimpleVector<Scalar>::import_from_file(const char *filename, const char *var_name, MatrixExportFormat fmt)
{
switch (fmt)
{
case EXPORT_FORMAT_PLAIN_ASCII:
{
std::vector<Scalar> data;
std::ifstream input(filename);
if (input.bad())
throw Exceptions::IOException(Exceptions::IOException::Read, filename);
std::string lineData;
while (getline(input, lineData))
{
Scalar d;
std::stringstream lineStream(lineData);
lineStream >> d;
data.push_back(d);
}
this->alloc(data.size());
memcpy(this->v, &data[0], sizeof(Scalar)*data.size());
}
break;
case EXPORT_FORMAT_MATLAB_MATIO:
#ifdef WITH_MATIO
mat_t *matfp;
matvar_t *matvar;
matfp = Mat_Open(filename, MAT_ACC_RDONLY);
if (!matfp)
{
throw Exceptions::IOException(Exceptions::IOException::Read, filename);
return;
}
matvar = Mat_VarRead(matfp, var_name);
if (matvar)
{
this->alloc(matvar->dims[0]);
if (Hermes::Helpers::TypeIsReal<Scalar>::value)
memcpy(this->v, matvar->data, sizeof(Scalar)*this->size);
else
{
std::complex<double>* complex_data = malloc_with_check<SimpleVector<Scalar>, std::complex<double> >(this->size, this);
double* real_array = (double*)((mat_complex_split_t*)matvar->data)->Re;
double* imag_array = (double*)((mat_complex_split_t*)matvar->data)->Im;
for (int i = 0; i < this->size; i++)
complex_data[i] = std::complex<double>(real_array[i], imag_array[i]);
memcpy(this->v, complex_data, sizeof(Scalar)*this->size);
free_with_check(complex_data);
}
}
Mat_Close(matfp);
if (!matvar)
throw Exceptions::IOException(Exceptions::IOException::Read, filename);
#else
throw Exceptions::Exception("MATIO not included.");
#endif
break;
case EXPORT_FORMAT_MATRIX_MARKET:
throw Hermes::Exceptions::MethodNotImplementedException("SimpleVector<Scalar>::import_from_file - Matrix Market");
break;
#ifdef WITH_BSON
case EXPORT_FORMAT_BSON:
{
FILE *fpr;
fpr = fopen(filename, "rb");
// file size:
fseek(fpr, 0, SEEK_END);
int size = ftell(fpr);
rewind(fpr);
// allocate memory to contain the whole file:
char *datar = malloc_with_check<char>(size);
fread(datar, size, 1, fpr);
fclose(fpr);
bson br;
bson_init_finished_data(&br, datar, 0);
bson_iterator it;
bson sub;
bson_find(&it, &br, "size");
this->size = bson_iterator_int(&it);
this->v = malloc_with_check<SimpleVector<Scalar>, Scalar>(this->size, this);
bson_iterator it_coeffs;
bson_find(&it_coeffs, &br, "v");
bson_iterator_subobject_init(&it_coeffs, &sub, 0);
bson_iterator_init(&it, &sub);
int index_coeff = 0;
while (bson_iterator_next(&it))
this->v[index_coeff++] = bson_iterator_double(&it);
if (!Hermes::Helpers::TypeIsReal<Scalar>::value)
{
bson_find(&it_coeffs, &br, "v-imag");
bson_iterator_subobject_init(&it_coeffs, &sub, 0);
bson_iterator_init(&it, &sub);
index_coeff = 0;
while (bson_iterator_next(&it))
((std::complex<double>)this->v[index_coeff++]).imag(bson_iterator_double(&it));
}
bson_destroy(&br);
free_with_check(datar);
}
break;
#endif
}
}
void SimpleVector<Scalar>::import_from_file(const char *filename, const char *var_name, MatrixExportFormat fmt)
{
switch (fmt)
{
case EXPORT_FORMAT_PLAIN_ASCII:
{
std::vector<Scalar> data;
std::ifstream input (filename);
if(input.bad())
throw Exceptions::IOException(Exceptions::IOException::Read, filename);
std::string lineData;
while(getline(input, lineData))
{
Scalar d;
std::stringstream lineStream(lineData);
lineStream >> d;
data.push_back(d);
}
this->alloc(data.size());
memcpy(this->v, &data[0], sizeof(Scalar)*data.size());
}
break;
case EXPORT_FORMAT_MATLAB_MATIO:
#ifdef WITH_MATIO
mat_t *matfp;
matvar_t *matvar;
matfp = Mat_Open(filename,MAT_ACC_RDONLY);
if (!matfp )
{
throw Exceptions::IOException(Exceptions::IOException::Read, filename);
return;
}
matvar = Mat_VarRead(matfp, var_name);
if (matvar)
{
this->alloc(matvar->dims[0]);
if(Hermes::Helpers::TypeIsReal<Scalar>::value)
memcpy(this->v, matvar->data, sizeof(Scalar)*this->size);
else
{
std::complex<double>* complex_data = new std::complex<double>[this->size];
double* real_array = (double*)((mat_complex_split_t*)matvar->data)->Re;
double* imag_array = (double*)((mat_complex_split_t*)matvar->data)->Im;
for(int i = 0; i < this->size; i++)
complex_data[i] = std::complex<double>(real_array[i], imag_array[i]);
memcpy(this->v, complex_data, sizeof(Scalar)*this->size);
delete [] complex_data;
}
}
Mat_Close(matfp);
if(!matvar)
throw Exceptions::IOException(Exceptions::IOException::Read, filename);
#else
throw Exceptions::Exception("MATIO not included.");
#endif
break;
case EXPORT_FORMAT_MATRIX_MARKET:
throw Hermes::Exceptions::MethodNotImplementedException("SimpleVector<Scalar>::import_from_file - Matrix Market");
}
}
void SimpleVector<Scalar>::export_to_file(const char *filename, const char *var_name, MatrixExportFormat fmt, char* number_format)
{
if(!v)
throw Exceptions::MethodNotOverridenException("Vector<Scalar>::export_to_file");
switch (fmt)
{
case EXPORT_FORMAT_MATRIX_MARKET:
{
FILE* file = fopen(filename, "w");
if(!file)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
if(Hermes::Helpers::TypeIsReal<Scalar>::value)
fprintf(file, "%%%%Matrix<Scalar>Market matrix coordinate real\n");
else
fprintf(file, "%%%%Matrix<Scalar>Market matrix coordinate complex\n");
fprintf(file, "%d 1 %d\n", this->size, this->size);
for (unsigned int j = 0; j < this->size; j++)
{
Hermes::Helpers::fprint_coordinate_num(file, j + 1, 1, v[j], number_format);
fprintf(file, "\n");
}
fclose(file);
}
break;
case EXPORT_FORMAT_MATLAB_MATIO:
{
#ifdef WITH_MATIO
size_t dims[2];
dims[0] = this->size;
dims[1] = 1;
mat_t *mat = Mat_CreateVer(filename, "", MAT_FT_MAT5);
matvar_t *matvar;
// For complex.
double* v_re = nullptr;
double* v_im = nullptr;
void* data;
if(Hermes::Helpers::TypeIsReal<Scalar>::value)
{
data = v;
matvar = Mat_VarCreate(var_name, MAT_C_DOUBLE, MAT_T_DOUBLE, 2, dims, data, MAT_F_DONT_COPY_DATA);
}
else
{
v_re = new double[this->size];
v_im = new double[this->size];
struct mat_complex_split_t z = {v_re, v_im};
for(int i = 0; i < this->size; i++)
{
v_re[i] = ((std::complex<double>)(this->v[i])).real();
v_im[i] = ((std::complex<double>)(this->v[i])).imag();
data = &z;
}
matvar = Mat_VarCreate(var_name, MAT_C_DOUBLE, MAT_T_DOUBLE, 2, dims, data, MAT_F_DONT_COPY_DATA | MAT_F_COMPLEX);
}
if (matvar)
{
Mat_VarWrite(mat, matvar, MAT_COMPRESSION_ZLIB);
Mat_VarFree(matvar);
}
if(v_re)
delete [] v_re;
if(v_im)
delete [] v_im;
Mat_Close(mat);
if(!matvar)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
#else
throw Exceptions::Exception("MATIO not included.");
#endif
}
break;
case EXPORT_FORMAT_PLAIN_ASCII:
{
FILE* file = fopen(filename, "w");
if(!file)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
for (unsigned int i = 0; i < this->size; i++)
{
Hermes::Helpers::fprint_num(file, v[i], number_format);
fprintf(file, "\n");
}
fclose(file);
}
}
}
void CSMatrix<Scalar>::export_to_file(const char *filename, const char *var_name, MatrixExportFormat fmt, char* number_format, bool invert_storage)
{
switch (fmt)
{
case EXPORT_FORMAT_MATRIX_MARKET:
{
FILE* file = fopen(filename, "w");
if(!file)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
if(Hermes::Helpers::TypeIsReal<Scalar>::value)
fprintf(file, "%%%%Matrix<Scalar>Market matrix coordinate real\n");
else
fprintf(file, "%%%%Matrix<Scalar>Market matrix coordinate complex\n");
fprintf(file, "%d %d %d\n", this->size, this->size, this->nnz);
if(invert_storage)
this->switch_orientation();
for (unsigned int j = 0; j < this->size; j++)
{
for (int i = Ap[j]; i < Ap[j + 1]; i++)
{
Hermes::Helpers::fprint_coordinate_num(file, i_coordinate(Ai[i] + 1, j + 1, invert_storage), j_coordinate(Ai[i] + 1, j + 1, invert_storage), Ax[i], number_format);
fprintf(file, "\n");
}
}
if(invert_storage)
this->switch_orientation();
fclose(file);
}
break;
case EXPORT_FORMAT_MATLAB_MATIO:
{
#ifdef WITH_MATIO
mat_sparse_t sparse;
sparse.nzmax = this->nnz;
if(invert_storage)
this->switch_orientation();
sparse.nir = this->nnz;
sparse.ir = Ai;
sparse.njc = this->size + 1;
sparse.jc = (int *) Ap;
sparse.ndata = this->nnz;
size_t dims[2];
dims[0] = this->size;
dims[1] = this->size;
mat_t *mat = Mat_CreateVer(filename, "", MAT_FT_MAT5);
matvar_t *matvar;
// For complex. No allocation here.
double* Ax_re = nullptr;
double* Ax_im = nullptr;
// For real.
if(Hermes::Helpers::TypeIsReal<Scalar>::value)
{
sparse.data = Ax;
matvar = Mat_VarCreate(var_name, MAT_C_SPARSE, MAT_T_DOUBLE, 2, dims, &sparse, MAT_F_DONT_COPY_DATA);
}
else
{
// For complex.
Ax_re = new double[this->nnz];
Ax_im = new double[this->nnz];
struct mat_complex_split_t z = {Ax_re, Ax_im};
for(int i = 0; i < this->nnz; i++)
{
Ax_re[i] = ((std::complex<double>)(this->Ax[i])).real();
Ax_im[i] = ((std::complex<double>)(this->Ax[i])).imag();
sparse.data = &z;
}
matvar = Mat_VarCreate(var_name, MAT_C_SPARSE, MAT_T_DOUBLE, 2, dims, &sparse, MAT_F_DONT_COPY_DATA | MAT_F_COMPLEX);
}
if (matvar)
{
Mat_VarWrite(mat, matvar, MAT_COMPRESSION_ZLIB);
Mat_VarFree(matvar);
}
if(invert_storage)
this->switch_orientation();
if(Ax_re)
delete [] Ax_re;
if(Ax_im)
delete [] Ax_im;
Mat_Close(mat);
if(!matvar)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
#endif
}
break;
case EXPORT_FORMAT_PLAIN_ASCII:
{
FILE* file = fopen(filename, "w");
if(!file)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
if(invert_storage)
this->switch_orientation();
for (unsigned int j = 0; j < this->size; j++)
{
for (int i = Ap[j]; i < Ap[j + 1]; i++)
{
Helpers::fprint_coordinate_num(file, i_coordinate(Ai[i], j, invert_storage), j_coordinate(Ai[i], j, invert_storage), Ax[i], number_format);
fprintf(file, "\n");
}
}
if(invert_storage)
this->switch_orientation();
fclose(file);
}
}
}
void CSMatrix<Scalar>::export_to_file(const char *filename, const char *var_name, MatrixExportFormat fmt, char* number_format, bool invert_storage)
{
switch (fmt)
{
case EXPORT_FORMAT_MATRIX_MARKET:
{
FILE* file = fopen(filename, "w");
if (!file)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
if (Hermes::Helpers::TypeIsReal<Scalar>::value)
fprintf(file, "%%%%MatrixMarket matrix coordinate real general\n");
else
fprintf(file, "%%%%MatrixMarket matrix coordinate complex general\n");
fprintf(file, "%d %d %d\n", this->size, this->size, this->nnz);
if (invert_storage)
this->switch_orientation();
for (unsigned int j = 0; j < this->size; j++)
{
for (int i = Ap[j]; i < Ap[j + 1]; i++)
{
Hermes::Helpers::fprint_coordinate_num(file, i_coordinate(Ai[i] + 1, j + 1, invert_storage), j_coordinate(Ai[i] + 1, j + 1, invert_storage), Ax[i], number_format);
fprintf(file, "\n");
}
}
if (invert_storage)
this->switch_orientation();
fclose(file);
}
break;
case EXPORT_FORMAT_MATLAB_MATIO:
{
#ifdef WITH_MATIO
mat_sparse_t sparse;
sparse.nzmax = this->nnz;
if (invert_storage)
this->switch_orientation();
sparse.nir = this->nnz;
sparse.ir = Ai;
sparse.njc = this->size + 1;
sparse.jc = (int *)Ap;
sparse.ndata = this->nnz;
size_t dims[2];
dims[0] = this->size;
dims[1] = this->size;
mat_t *mat = Mat_CreateVer(filename, "", MAT_FT_MAT5);
matvar_t *matvar;
// For complex. No allocation here.
double* Ax_re = nullptr;
double* Ax_im = nullptr;
// For real.
if (Hermes::Helpers::TypeIsReal<Scalar>::value)
{
sparse.data = Ax;
matvar = Mat_VarCreate(var_name, MAT_C_SPARSE, MAT_T_DOUBLE, 2, dims, &sparse, MAT_F_DONT_COPY_DATA);
}
else
{
// For complex.
Ax_re = malloc_with_check<CSMatrix<Scalar>, double>(this->nnz, this);
Ax_im = malloc_with_check<CSMatrix<Scalar>, double>(this->nnz, this);
struct mat_complex_split_t z = { Ax_re, Ax_im };
for (int i = 0; i < this->nnz; i++)
{
Ax_re[i] = ((std::complex<double>)(this->Ax[i])).real();
Ax_im[i] = ((std::complex<double>)(this->Ax[i])).imag();
sparse.data = &z;
}
matvar = Mat_VarCreate(var_name, MAT_C_SPARSE, MAT_T_DOUBLE, 2, dims, &sparse, MAT_F_DONT_COPY_DATA | MAT_F_COMPLEX);
}
if (matvar)
{
Mat_VarWrite(mat, matvar, MAT_COMPRESSION_ZLIB);
Mat_VarFree(matvar);
}
if (invert_storage)
this->switch_orientation();
free_with_check(Ax_re);
free_with_check(Ax_im);
Mat_Close(mat);
if (!matvar)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
#endif
}
break;
case EXPORT_FORMAT_PLAIN_ASCII:
{
FILE* file = fopen(filename, "w");
if (!file)
throw Exceptions::IOException(Exceptions::IOException::Write, filename);
if (invert_storage)
this->switch_orientation();
for (unsigned int j = 0; j < this->size; j++)
{
for (int i = Ap[j]; i < Ap[j + 1]; i++)
{
Helpers::fprint_coordinate_num(file, i_coordinate(Ai[i], j, invert_storage), j_coordinate(Ai[i], j, invert_storage), Ax[i], number_format);
fprintf(file, "\n");
}
}
if (invert_storage)
this->switch_orientation();
fclose(file);
}
break;
#ifdef WITH_BSON
case EXPORT_FORMAT_BSON:
{
// Init bson
bson bw;
bson_init(&bw);
// Matrix size.
bson_append_int(&bw, "size", this->size);
// Nonzeros.
bson_append_int(&bw, "nnz", this->nnz);
if (invert_storage)
this->switch_orientation();
bson_append_start_array(&bw, "Ap");
for (unsigned int i = 0; i < this->size; i++)
bson_append_int(&bw, "p", this->Ap[i]);
bson_append_finish_array(&bw);
bson_append_start_array(&bw, "Ai");
for (unsigned int i = 0; i < this->nnz; i++)
bson_append_int(&bw, "i", this->Ai[i]);
bson_append_finish_array(&bw);
bson_append_start_array(&bw, "Ax");
for (unsigned int i = 0; i < this->nnz; i++)
bson_append_double(&bw, "x", real(this->Ax[i]));
bson_append_finish_array(&bw);
if (!Hermes::Helpers::TypeIsReal<Scalar>::value)
{
bson_append_start_array(&bw, "Ax-imag");
for (unsigned int i = 0; i < this->nnz; i++)
bson_append_double(&bw, "x-i", imag(this->Ax[i]));
bson_append_finish_array(&bw);
}
bson_append_finish_array(&bw);
if (invert_storage)
this->switch_orientation();
// Done.
bson_finish(&bw);
// Write to disk.
FILE *fpw;
fpw = fopen(filename, "wb");
const char *dataw = (const char *)bson_data(&bw);
fwrite(dataw, bson_size(&bw), 1, fpw);
fclose(fpw);
bson_destroy(&bw);
}
break;
#endif
}
}
int
main(int argc, char **argv)
{
char *mdf_filename = NULL;
char *mat_filename = NULL;
const mdf_t *mdf;
filter_t *filter;
char *filter_filename = NULL;
char *program_name = argv[0];
/* parse arguments */
while (1) {
static struct option long_options[] = {
/* These options set a flag. */
{"verbose", no_argument, &verbose_level, 1},
{"debug", no_argument, &verbose_level, 2},
{"deep", no_argument, &verbose_level, 3},
{"brief", no_argument, &verbose_level, 0},
{"v5", no_argument, &mat_file_ver, (int)MAT_FT_MAT5},
{"v73", no_argument, &mat_file_ver, (int)MAT_FT_MAT73},
{"compress",no_argument, NULL, 'z'},
/* These options don't set a flag.
We distinguish them by their indices. */
{"filter", required_argument, 0, (int)'f'},
{"help", no_argument, NULL, (int)'h'},
{0, 0, 0, 0}
};
/* getopt_long stores the option index here. */
int option_index = 0;
int c;
c = getopt_long (argc, argv, "a:b:d:f:hm:t:vz",
long_options, &option_index);
/* Detect the end of the options. */
if (c == -1) break;
switch (c) {
case 0:
break;
case 'f':
filter_filename = optarg;
break;
case 'h':
help(program_name);
exit(EXIT_SUCCESS);
break;
case 'v':
verbose_level = 1;
break;
case 'd':
verbose_level = 2;
break;
case 'z':
mdftomat.compress = MAT_COMPRESSION_ZLIB;
break;
case '?':
/* getopt_long already printed an error message. */
usage_error(program_name);
break;
default:
fprintf(stderr, "error: unknown option %c\n", c);
usage_error(program_name);
}
}
/* check structure packing */
assert(offsetof(cn_block_t,link_asam_mcd_name) == 218);
/* input files */
if (optind == argc - 2) {
mdf_filename = argv[optind++];
mat_filename = argv[optind++];
} else {
fprintf(stderr, "error: wrong number of arguments\n");
usage_error(program_name);
return 1;
}
/* print banner */
if(verbose_level >= 1) {
fprintf(stderr, "%s (%s, %s, cantools " PACKAGE_VERSION ")\n",
program_name, __DATE__, __TIME__);
}
/* connect to mdf file */
mdf = mdf_attach(mdf_filename, verbose_level);
if(mdf == NULL) {
return 1;
}
/* create mat file */
mdftomat.mat = Mat_CreateVer(mat_filename, NULL, (enum mat_ft)mat_file_ver);
if(mdftomat.mat == NULL) {
fprintf(stderr,"can't write to mat file %s\n",mat_filename);
return 1;
}
/* read filter */
if(filter_filename != NULL) {
filter = mdf_filter_create(filter_filename);
if(filter == NULL) {
return 1;
}
} else {
filter = NULL;
}
/* process MDF file */
if(verbose_level >= 1) {
fprintf(stderr, "converting %s to %sfile %s\n",
mdf_filename,
(mdftomat.compress == MAT_COMPRESSION_ZLIB)?"compressed ":"",
mat_filename);
}
mdfProcess(mdf, &mdftomat, filter);
/* free filter */
filter_free(filter);
/* detach from mdf file */
mdf_detach(mdf);
/* close mat file */
Mat_Close(mdftomat.mat);
/* say goodbye */
if(verbose_level >= 1) {
puts("done.");
}
return 0;
}
void CSMatrix<Scalar>::import_from_file(const char *filename, const char *var_name, MatrixExportFormat fmt, bool invert_storage)
{
this->free();
switch (fmt)
{
case EXPORT_FORMAT_MATRIX_MARKET:
throw Exceptions::MethodNotOverridenException("CSMatrix<Scalar>::import_from_file - Matrix Market");
break;
case EXPORT_FORMAT_MATLAB_MATIO:
{
#ifdef WITH_MATIO
mat_t *matfp;
matvar_t *matvar;
matfp = Mat_Open(filename, MAT_ACC_RDONLY);
if (!matfp)
throw Exceptions::IOException(Exceptions::IOException::Read, filename);
matvar = Mat_VarRead(matfp, var_name);
if (matvar)
{
mat_sparse_t *sparse = (mat_sparse_t *)matvar->data;
this->nnz = sparse->nir;
this->Ax = malloc_with_check<CSMatrix<Scalar>, Scalar>(this->nnz, this);
this->Ai = malloc_with_check<CSMatrix<Scalar>, int>(this->nnz, this);
this->size = sparse->njc;
this->Ap = malloc_with_check<CSMatrix<Scalar>, int>(this->size + 1, this);
void* data = nullptr;
if (Hermes::Helpers::TypeIsReal<Scalar>::value)
data = sparse->data;
else
{
std::complex<double>* complex_data = malloc_with_check<CSMatrix<Scalar>, std::complex<double> >(this->nnz, this);
double* real_array = (double*)((mat_complex_split_t*)sparse->data)->Re;
double* imag_array = (double*)((mat_complex_split_t*)sparse->data)->Im;
for (int i = 0; i < this->nnz; i++)
complex_data[i] = std::complex<double>(real_array[i], imag_array[i]);
data = (void*)complex_data;
}
memcpy(this->Ax, data, this->nnz * sizeof(Scalar));
if (!Hermes::Helpers::TypeIsReal<Scalar>::value)
free_with_check(data);
memcpy(this->Ap, sparse->jc, this->size * sizeof(int));
this->Ap[this->size] = this->nnz;
memcpy(this->Ai, sparse->ir, this->nnz * sizeof(int));
if (invert_storage)
this->switch_orientation();
}
Mat_Close(matfp);
if (!matvar)
throw Exceptions::IOException(Exceptions::IOException::Read, filename);
#else
throw Exceptions::Exception("MATIO not included.");
#endif
}
break;
case EXPORT_FORMAT_PLAIN_ASCII:
throw Exceptions::MethodNotOverridenException("CSMatrix<Scalar>::import_from_file - Simple format");
#ifdef WITH_BSON
case EXPORT_FORMAT_BSON:
{
FILE *fpr;
fpr = fopen(filename, "rb");
// file size:
fseek(fpr, 0, SEEK_END);
int size = ftell(fpr);
rewind(fpr);
// allocate memory to contain the whole file:
char *datar = malloc_with_check<char>(size);
fread(datar, size, 1, fpr);
fclose(fpr);
bson br;
bson_init_finished_data(&br, datar, 0);
bson_iterator it;
bson sub;
bson_find(&it, &br, "size");
this->size = bson_iterator_int(&it);
bson_find(&it, &br, "nnz");
this->nnz = bson_iterator_int(&it);
this->Ap = malloc_with_check<CSMatrix<Scalar>, int>(this->size + 1, this);
this->Ai = malloc_with_check<CSMatrix<Scalar>, int>(nnz, this);
this->Ax = malloc_with_check<CSMatrix<Scalar>, Scalar>(nnz, this);
// coeffs
bson_iterator it_coeffs;
bson_find(&it_coeffs, &br, "Ap");
bson_iterator_subobject_init(&it_coeffs, &sub, 0);
bson_iterator_init(&it, &sub);
int index_coeff = 0;
while (bson_iterator_next(&it))
this->Ap[index_coeff++] = bson_iterator_int(&it);
this->Ap[this->size] = this->nnz;
bson_find(&it_coeffs, &br, "Ai");
bson_iterator_subobject_init(&it_coeffs, &sub, 0);
bson_iterator_init(&it, &sub);
index_coeff = 0;
while (bson_iterator_next(&it))
this->Ai[index_coeff++] = bson_iterator_int(&it);
bson_find(&it_coeffs, &br, "Ax");
bson_iterator_subobject_init(&it_coeffs, &sub, 0);
bson_iterator_init(&it, &sub);
index_coeff = 0;
while (bson_iterator_next(&it))
this->Ax[index_coeff++] = bson_iterator_double(&it);
if (!Hermes::Helpers::TypeIsReal<Scalar>::value)
{
bson_find(&it_coeffs, &br, "Ax-imag");
bson_iterator_subobject_init(&it_coeffs, &sub, 0);
bson_iterator_init(&it, &sub);
index_coeff = 0;
while (bson_iterator_next(&it))
((std::complex<double>)this->Ax[index_coeff++]).imag(bson_iterator_double(&it));
}
if (invert_storage)
this->switch_orientation();
bson_destroy(&br);
free_with_check(datar);
}
#endif
break;
}
}
void Job::run(){
if (Print)
cout << endl << "------ new run ------ iRip==" << iRip << endl << endl;
//
int iTr=0,iTs=0,iVar,iV,iFRip,
i,ii,
trsz=ds.pr->TrSzD, tssz=ds.pr->TsSzD, valdim=ds.LabelValSelSize;
double acc[trsz][tssz][FRip], mse[trsz][tssz][FRip], scc[trsz][tssz][FRip],
featNum[FeatSelSize][FRip],
*res,trends[valdim][trsz][FRip],actualLabel[valdim],ValidTrend[valdim];
matvar_t *varnameC;
//
for (iVar=0; iVar<LabelSelSize; ++iVar){
iV=LabelSelIdx[iVar]; // questa e` la variabile che vogliamo decodificare
// -------------- cambio il nome del file in modo da coincidere con la variabile --------------------------------------
string resFile_=resFile,VARNAME; // cosi` lo scope e` locale in questo ciclo
varnameC = Mat_VarGetCell(VARIABLEs,iV); // recupero il nome di questa variabile
VARNAME=(const char*)varnameC->data;
// segnalo dove sono a video
if (Print)
cout << endl << "------ iV=" << VARNAME << endl << endl;
//
resFile_+=VARNAME; resFile_+="-"; // riporto quale variabile sto esaminando nel filename
resFile_+="nF_"; resFile_+=to_string(FeatSelSize); resFile_+="-"; // e quante features
resFile_+="res.mat"; // aggiungo l'estensione
// elimino gli spazi
resFile_.erase(remove_if(resFile_.begin(),
resFile_.end(),
[](char x){return isspace(x);}),
resFile_.end());
// --------------------------------------------------------------------------------------------------------------------
//
// ---------------------------- recupero l'andamento della label sul validation set ----------------------------------
for (ii=0; ii<valdim; ++ii){
i=ds.label_valid_selection[ii];
actualLabel[ii]=labels[LabelSize[0]*iV+i]; // prendo l'i-esimo indice del del validation set della variabile iV
// LabelSize[0] e` il numero totale delle istanze
}
// ---------------------------------------------------------------------------------------------------------------------
//
for (iTr=0; iTr<trsz; ++iTr){
ds.assegnoTrainingSet(iTr);
for (iFRip=0; iFRip<FRip; ++iFRip){
if (Print)
cout << endl << "------ iTr%=" << (double)iTr/trsz
<< endl << "------ iFRip%=" << (double)iFRip/FRip
<< endl << endl;
UpdateFeatureSelection(); // cambio, se devo, la selezione delle features
//
// ----------------------------------------- recupero gli indici delle features ---------------------------------------
for (i=0; i<FeatSelSize; ++i) // recupero gli indici delle feature che ho usato
featNum[i][iFRip]=(double)(feature_sel[i]+1); // per metterla nel ws di matio
// aggiungo 1.0 per come funziona l'indicizzazione su matlab
// ---------------------------------------------------------------------------------------------------------------------
//
// per debug
if (0){
cout << endl << "feat idx" << endl;
for (int i=0; i<FeatSelSize; ++i)
cout << " " << feature_sel[i];
cout << endl;
}
assegnato_svm=false; // devo riaddestrare per ogni Training Set o per ogni sottocampionamento delle features
TrainingFromAssignedProblem(iV); // addestro con lo stesso Training Set ma (forse) diverse Features
predictValidationSet(ValidTrend,iV); // Test sul Validation Set
// ------------------------------- recupero i trends sul Validation Set -----------------------------------------
for (ii=0; ii<valdim; ++ii)
trends[ii][iTr][iFRip]=ValidTrend[ii];
// --------------------------------------------------------------------------------------------------------------
//
for (iTs=0; iTs<tssz; ++iTs){
ds.assegnoTestSet(iTs);
predictTestSet(iV);
// recupero le performance del modello
res = (double *)((matvar_t *)RES[1])->data;
acc[iTr][iTs][iFRip]=res[0];
mse[iTr][iTs][iFRip]=res[1];
scc[iTr][iTs][iFRip]=res[2];
}
}
}
// -------------- salvo un file per ogni variabile | setto il workspace da salvare --------------------------------------
int WsSize=12;
matvar_t *workspace[WsSize];
size_t dims_3[3], dims_2[2], dims_1[1];
dims_3[2]=trsz; dims_3[1]=tssz; dims_3[0]=FRip;
dims_2[1]=FeatSelSize; dims_2[0]=FRip;
dims_1[0]=1;
workspace[0] = Mat_VarCreate("acc",MAT_C_DOUBLE,MAT_T_DOUBLE,3,dims_3,acc,0);
workspace[1] = Mat_VarCreate("mse",MAT_C_DOUBLE,MAT_T_DOUBLE,3,dims_3,mse,0);
workspace[2] = Mat_VarCreate("scc",MAT_C_DOUBLE,MAT_T_DOUBLE,3,dims_3,scc,0);
workspace[3] = Mat_VarCreate("featIdx",MAT_C_DOUBLE,MAT_T_DOUBLE,2,dims_2,featNum,0);
dims_2[1]=valdim; dims_2[0]=1;
workspace[4] = Mat_VarCreate("actualLabel",MAT_C_DOUBLE,MAT_T_DOUBLE,2,dims_2,actualLabel,0);
dims_3[2]=valdim; dims_3[1]=trsz; dims_3[0]=FRip;
workspace[5] = Mat_VarCreate("trends",MAT_C_DOUBLE,MAT_T_DOUBLE,3,dims_3,trends,0);
double FRip_ws[1], trsz_ws[1], tssz_ws[1], FeatSelSize_ws[1], validSz_ws[1];
FRip_ws[0]=FRip; trsz_ws[0]=trsz; tssz_ws[0]=tssz; FeatSelSize_ws[0]=FeatSelSize; validSz_ws[0]=valdim;
workspace[6] = Mat_VarCreate("FeatSelectionRip",MAT_C_DOUBLE,MAT_T_DOUBLE,1,dims_1,FRip_ws,0);
workspace[7] = Mat_VarCreate("NumFeatures",MAT_C_DOUBLE,MAT_T_DOUBLE,1,dims_1,FeatSelSize_ws,0);
workspace[8] = Mat_VarCreate("TrSz",MAT_C_DOUBLE,MAT_T_DOUBLE,1,dims_1,trsz_ws,0);
workspace[9] = Mat_VarCreate("TsSz",MAT_C_DOUBLE,MAT_T_DOUBLE,1,dims_1,tssz_ws,0);
workspace[10] = Mat_VarCreate("ValidationSetSize",MAT_C_DOUBLE,MAT_T_DOUBLE,1,dims_1,validSz_ws,0);
string help ="CONTENUTO DEL MATFILE:\n";
help+="{acc,mse,scc}\n";
help+="\tdimensione RxTsxTr\n";
help+="\t(accuratezza,mean squared error ed r2\n\toutput di libsvm)\n";
help+="featIdx\n";
help+="\tdimensione RxN\n";
help+="\t(indice delle features usate per addestrare\n\t il modello ad ogni ricampionamento)\n";
help+="actualLabel\n";
help+="\tdimensione 1xV\n";
help+="\t(valore della label corrispondente al validation set\n\tNB: salvo un file diverso per ogni label)\n";
help+="trends\n";
help+="\tdimensione RxTrxV\n";
help+="\t(predizione della label, ne ho una diverso per ogni modello\n\tNB: ho un modello diverso per ogni\n\t +ricampionamento delle features\n\t +ricampionamento del training set)\n";
help+="***LEGENDA***\n";
help+="\tR=FeatSelectionRip\n";
help+="\tTs=TsSz\n";
help+="\tTr=TrSz\n";
help+="\tN=NumFeatures\n";
help+="\tV=ValidationSetSize\n";
dims_2[1]=help.size(); dims_2[0]=1;
workspace[11] = Mat_VarCreate("README",MAT_C_CHAR,MAT_T_UINT8,2,dims_2,(char*)help.c_str(),0);
// Apro scrivo e chiudo il matfile
mat_t *Out_MATFILE = Mat_CreateVer((const char*)resFile_.c_str(),NULL,MAT_FT_DEFAULT);
for (int iWS=0; iWS<WsSize; ++iWS)
Mat_VarWrite(Out_MATFILE, workspace[iWS], MAT_COMPRESSION_NONE);
Mat_Close(Out_MATFILE);
// ----------------------------------------------------------------------------------------------------------------------
}
return;
}
void CSMatrix<Scalar>::import_from_file(const char *filename, const char *var_name, MatrixExportFormat fmt, bool invert_storage)
{
switch (fmt)
{
case EXPORT_FORMAT_MATRIX_MARKET:
throw Exceptions::MethodNotOverridenException("CSMatrix<Scalar>::import_from_file - Matrix Market");
break;
case EXPORT_FORMAT_MATLAB_MATIO:
{
#ifdef WITH_MATIO
mat_t *matfp;
matvar_t *matvar;
matfp = Mat_Open(filename,MAT_ACC_RDONLY);
if (!matfp )
{
throw Exceptions::IOException(Exceptions::IOException::Read, filename);
return;
}
matvar = Mat_VarRead(matfp, var_name);
if (matvar)
{
mat_sparse_t *sparse = (mat_sparse_t *)matvar->data;
this->nnz = sparse->nir;
this->Ax = new Scalar[this->nnz];
this->Ai = new int[this->nnz];
this->size = sparse->njc - 1;
this->Ap = new int[this->size + 1];
void* data = nullptr;
if(Hermes::Helpers::TypeIsReal<Scalar>::value)
data = sparse->data;
else
{
std::complex<double>* complex_data = new std::complex<double>[this->nnz];
double* real_array = (double*)((mat_complex_split_t*)sparse->data)->Re;
double* imag_array = (double*)((mat_complex_split_t*)sparse->data)->Im;
for(int i = 0; i < this->nnz; i++)
complex_data[i] = std::complex<double>(real_array[i], imag_array[i]);
data = (void*)complex_data;
}
memcpy(this->Ax, data, this->nnz * sizeof(Scalar));
if(!Hermes::Helpers::TypeIsReal<Scalar>::value)
delete [] data;
memcpy(this->Ap, sparse->jc, (this->size + 1) * sizeof(Scalar));
memcpy(this->Ai, sparse->ir, this->nnz * sizeof(int));
if(invert_storage)
this->switch_orientation();
}
Mat_Close(matfp);
if(!matvar)
throw Exceptions::IOException(Exceptions::IOException::Read, filename);
#else
throw Exceptions::Exception("MATIO not included.");
#endif
}
break;
case EXPORT_FORMAT_PLAIN_ASCII:
throw Exceptions::MethodNotOverridenException("CSMatrix<Scalar>::import_from_file - Simple format");
break;
}
}
G_MODULE_EXPORT void save_as(const char *filename, int type)
{
FILE *fp;
unsigned int i, j;
double freq, k;
mat_t *mat;
matvar_t *matvar;
int dims[2];
char tmp[20];
GdkPixbuf *pixbuf;
GError *err=NULL;
GdkColormap *cmap;
gint width, height;
gboolean ret = true;
char *name;
gdouble *tmp_data;
name = malloc(strlen(filename) + 5);
switch(type) {
/* Response Codes encoded in glade file */
case GTK_RESPONSE_DELETE_EVENT:
case GTK_RESPONSE_CANCEL:
break;
case SAVE_VSA:
/* Allow saving data when only in Time Domanin */
if ((gtk_combo_box_get_active(GTK_COMBO_BOX(plot_domain)) != TIME_PLOT) &&
(gtk_combo_box_get_active(GTK_COMBO_BOX(plot_domain)) != XY_PLOT)) {
create_blocking_popup(GTK_MESSAGE_WARNING, GTK_BUTTONS_CLOSE, "Invalid Plot Type",
"Please make sure to set the Plot Type to \"Time Domanin\" before saving data.");
return;
}
/* Save as Agilent VSA formatted file */
if (!strncasecmp(&filename[strlen(filename)-4], ".txt", 4))
strcpy(name, filename);
else
sprintf(name, "%s.txt", filename);
fp = fopen(name, "w");
if (!fp)
break;
fprintf(fp, "InputZoom\tTRUE\n");
fprintf(fp, "InputCenter\t0\n");
fprintf(fp, "InputRange\t1\n");
fprintf(fp, "InputRefImped\t50\n");
fprintf(fp, "XStart\t0\n");
if (!strcmp(adc_scale, "M"))
freq = adc_freq * 1000000;
else if (!strcmp(adc_scale, "k"))
freq = adc_freq * 1000;
else {
printf("error in writing\n");
break;
}
fprintf(fp, "XDelta\t%-.17f\n", 1.0/freq);
fprintf(fp, "XDomain\t2\n");
fprintf(fp, "XUnit\tSec\n");
fprintf(fp, "YUnit\tV\n");
fprintf(fp, "FreqValidMax\t%e\n", freq / 2);
fprintf(fp, "FreqValidMin\t-%e\n", freq / 2);
fprintf(fp, "Y\n");
for (j = 0; j < num_samples; j++) {
for (i = 0; i < num_active_channels ; i++) {
fprintf(fp, "%g", channel_data[i][j]);
if (i < (num_active_channels - 1))
fprintf(fp, "\t");
}
fprintf(fp, "\n");
}
fprintf(fp, "\n");
fclose(fp);
break;
case SAVE_MAT:
/* Allow saving data when only in Time Domanin */
if (gtk_combo_box_get_active(GTK_COMBO_BOX(plot_domain)) != TIME_PLOT) {
create_blocking_popup(GTK_MESSAGE_WARNING, GTK_BUTTONS_CLOSE, "Invalid Plot Type",
"Please make sure to set the Plot Type to \"Time Domanin\" before saving data.");
return;
}
/* Matlab file
* http://na-wiki.csc.kth.se/mediawiki/index.php/MatIO
*/
if (!strncasecmp(&filename[strlen(filename)-4], ".mat", 4))
strcpy(name, filename);
else
sprintf(name, "%s.mat", filename);
dims[1] = 1;
dims[0] = num_samples;
mat = Mat_Open(name, MAT_ACC_RDWR);
if(mat) {
for (i = 0; i < num_active_channels; i++) {
sprintf(tmp, "in_voltage%d", i);
if (!gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(save_mat_scale))) {
matvar = Mat_VarCreate(tmp, MAT_C_SINGLE,
MAT_T_SINGLE, 2, dims, channel_data[i], 0);
} else {
tmp_data = g_new(gdouble, num_samples);
if (channels[i].is_signed)
k = channels[i].bits_used - 1;
else
k = channels[i].bits_used;
for (j = 0; j < num_samples; j++) {
tmp_data[j] = (gdouble)channel_data[i][j] /
(pow(2.0, k));
}
matvar = Mat_VarCreate(tmp, MAT_C_DOUBLE,
MAT_T_DOUBLE, 2, dims, tmp_data, 0);
g_free(tmp_data);
}
if (!matvar)
printf("error creating matvar on channel %i\n", i);
else {
Mat_VarWrite(mat, matvar, 0);
Mat_VarFree(matvar);
}
}
Mat_Close(mat);
}
break;
case SAVE_CSV:
/* Allow saving data when only in Time Domanin */
if (gtk_combo_box_get_active(GTK_COMBO_BOX(plot_domain)) != TIME_PLOT) {
create_blocking_popup(GTK_MESSAGE_WARNING, GTK_BUTTONS_CLOSE, "Invalid Plot Type",
"Please make sure to set the Plot Type to \"Time Domanin\" before saving data.");
return;
}
/* save comma seperated valus (csv) */
if (!strncasecmp(&filename[strlen(filename)-4], ".csv", 4))
strcpy(name, filename);
else
sprintf(name, "%s.csv", filename);
fp = fopen(name, "w");
if (!fp)
break;
for (j = 0; j < num_samples; j++) {
for (i = 0; i < num_active_channels ; i++) {
fprintf(fp, "%g", channel_data[i][j]);
if (i < (num_active_channels - 1))
fprintf(fp, ", ");
}
fprintf(fp, "\n");
}
fprintf(fp, "\n");
fclose(fp);
break;
case SAVE_PNG:
/* save_png */
if (!strncasecmp(&filename[strlen(filename)-4], ".png", 4))
strcpy(name, filename);
else
sprintf(name, "%s.png", filename);
cmap = gdk_window_get_colormap(
GDK_DRAWABLE(gtk_widget_get_window(capture_graph)));
gdk_drawable_get_size(GDK_DRAWABLE(gtk_widget_get_window(capture_graph)),
&width, &height);
pixbuf = gdk_pixbuf_get_from_drawable(NULL,
GDK_DRAWABLE(gtk_widget_get_window(capture_graph)),
cmap, 0, 0, 0, 0, width, height);
if (pixbuf)
ret = gdk_pixbuf_save(pixbuf, name, "png", &err, NULL);
if (!pixbuf || !ret)
printf("error creating %s\n", name);
break;
default:
printf("ret : %i\n", ret);
}
free(name);
}
