From 842378276ab4c4a8dabd02324bb24b8da39c4384 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 18 Oct 2019 10:28:34 +0000
Subject: [PATCH] Done and implemented compression. It doesn't segfaults at the moment
---
src/snapshot.c | 18 +++-
src/io.c | 212 ++++++++++++++++++++++++++++++++++++++---------------
src/snapshot.h | 2
3 files changed, 166 insertions(+), 66 deletions(-)
diff --git a/src/io.c b/src/io.c
index 7a14447..0d22aa7 100644
--- a/src/io.c
+++ b/src/io.c
@@ -256,6 +256,9 @@
fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1)+vesicle->tlist->n);
fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"binary\">");
long *int_vector=(long *)malloc((vlist->n+monono*polyno+fonono*filno)*sizeof(long));
+ ts_double *float_vector=(double *)malloc((vlist->n+monono*polyno+fonono*filno)*sizeof(double));
+ ts_double *float_cell_vector=(double *)malloc((blist->n+monono*polyno+filno*(fonono-1)+vesicle->tlist->n)*sizeof(double));
+ ts_double *coordinate_vector=(double *)malloc(3*(vlist->n+monono*polyno+fonono*filno)*sizeof(double));
// sizes are as expected 4 bytes for int and 1 byte for char
// printf("size of ts_uint %ld, of int %ld, of char %ld",sizeof(ts_uint), sizeof(int), sizeof(char));
int offset=0;
@@ -288,26 +291,30 @@
}
}
printf("Offset in the end is %d, should be %d",offset,(vlist->n+monono*polyno+fonono*filno) );
- char *printout=ts_compress((char *)int_vector,offset*sizeof(long), offset);
+ char *printout=ts_compress((char *)int_vector,offset*sizeof(long));
fprintf(fh,"%s",printout);
free(printout);
fprintf(fh,"</DataArray>\n");
if(cstlist!=NULL){
- fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"ascii\">");
- for(i=0;i<vlist->n;i++){
+ fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"binary\">");
+ offset=0;
+ for(i=0;i<vlist->n;i++,offset++){
if(vtx[i]->cluster!=NULL){
- fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
+// fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
+ int_vector[offset]=vtx[i]->cluster->nvtx;
} else {
- fprintf(fh,"-1 ");
+// fprintf(fh,"-1 ");
+ int_vector[offset]=-1;
}
}
//polymeres
if(poly){
poly_idx=vlist->n;
for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
- fprintf(fh,"-1 ");
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++, offset++){
+ //fprintf(fh,"-1 ");
+ int_vector[offset]=-1;
}
}
}
@@ -315,12 +322,15 @@
if(fil){
poly_idx=vlist->n+monono*polyno;
for(i=0;i<vesicle->filament_list->n;i++){
- for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
- // fprintf(stderr,"was here\n");
- fprintf(fh,"-1 ");
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++, offset++){
+ // fprintf(fh,"-1 ");
+ int_vector[offset]=-1;
}
}
}
+ char *printout=ts_compress((char *)int_vector,offset*sizeof(long));
+ fprintf(fh,"%s",printout);
+ free(printout);
fprintf(fh,"</DataArray>\n");
@@ -328,16 +338,19 @@
}
//here comes additional data as needed. Currently only spontaneous curvature
- fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
- for(i=0;i<vlist->n;i++){
- fprintf(fh,"%.17e ",vtx[i]->c);
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"binary\">");
+ offset=0;
+ for(i=0;i<vlist->n;i++, offset++){
+// fprintf(fh,"%.17e ",vtx[i]->c);
+ float_vector[offset]=vtx[i]->c;
}
//polymeres
if(poly){
poly_idx=vlist->n;
for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
- fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++, offset++){
+ //fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
+ float_vector[offset]=vesicle->poly_list->poly[i]->vlist->vtx[j]->c;
}
}
}
@@ -345,25 +358,34 @@
if(fil){
poly_idx=vlist->n+monono*polyno;
for(i=0;i<vesicle->filament_list->n;i++){
- for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++,offset++){
// fprintf(stderr,"was here\n");
- fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
+ //fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
+ float_vector[offset]=vesicle->filament_list->poly[i]->vlist->vtx[j]->c;
}
}
}
+ printout=ts_compress((char *)float_vector,offset*sizeof(double));
+ fprintf(fh,"%s",printout);
+ free(printout);
+
+
fprintf(fh,"</DataArray>\n");
//here comes additional data. Energy!
- fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
- for(i=0;i<vlist->n;i++){
- fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"binary\">");
+ offset=0;
+ for(i=0;i<vlist->n;i++,offset++){
+// fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
+ float_vector[offset]=vtx[i]->energy*vtx[i]->xk;
}
//polymeres
if(poly){
poly_idx=vlist->n;
for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
- fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++,offset++){
+ //fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
+ float_vector[offset]=vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k;
}
}
}
@@ -371,68 +393,108 @@
if(fil){
poly_idx=vlist->n+monono*polyno;
for(i=0;i<vesicle->filament_list->n;i++){
- for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++,offset++){
// fprintf(stderr,"was here\n");
- fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
+// fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
+ float_vector[offset]=vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k;
}
}
}
+
+ printout=ts_compress((char *)float_vector,offset*sizeof(double));
+ fprintf(fh,"%s",printout);
+ free(printout);
+
fprintf(fh,"</DataArray>\n");
fprintf(fh,"</PointData>\n<CellData>\n");
if(vesicle->tape->stretchswitch==1){
- fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
- for(i=0;i<blist->n;i++){
- fprintf(fh, "0.0 ");
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"binary\">");
+ offset=0;
+ for(i=0;i<blist->n;i++,offset++){
+ //fprintf(fh, "0.0 ");
+ float_cell_vector[offset]=0.0;
}
- for(i=0;i<monono*polyno+filno*(fonono-1);i++){
- fprintf(fh,"0.0 ");
+ for(i=0;i<monono*polyno+filno*(fonono-1);i++,offset++){
+ float_cell_vector[offset]=0.0;
+ //fprintf(fh,"0.0 ");
}
- for(i=0;i<vesicle->tlist->n;i++){
- fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
+ for(i=0;i<vesicle->tlist->n;i++,offset++){
+ float_cell_vector[offset]=vesicle->tlist->tria[i]->energy;
+ //fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
}
+
+ printout=ts_compress((char *)float_cell_vector,offset*sizeof(double));
+ fprintf(fh,"%s",printout);
+ free(printout);
+
fprintf(fh,"</DataArray>\n");
}
- fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
- for(i=0;i<vlist->n;i++){
- fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
+ fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"binary\">\n");
+ offset=0;
+ for(i=0;i<vlist->n;i++,offset+=3){
+ //fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
+ coordinate_vector[offset]=vtx[i]->x;
+ coordinate_vector[offset+1]=vtx[i]->y;
+ coordinate_vector[offset+2]=vtx[i]->z;
}
//polymeres
if(poly){
for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
- fprintf(fh,"%.17e %.17e %.17e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,offset+=3){
+ //fprintf(fh,"%.17e %.17e %.17e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
+ coordinate_vector[offset]=vesicle->poly_list->poly[i]->vlist->vtx[j]->x;
+ coordinate_vector[offset+1]=vesicle->poly_list->poly[i]->vlist->vtx[j]->y;
+ coordinate_vector[offset+2]=vesicle->poly_list->poly[i]->vlist->vtx[j]->z;
}
}
}
//filaments
if(fil){
- for(i=0;i<vesicle->filament_list->n;i++){
+ for(i=0;i<vesicle->filament_list->n;i++,offset+=3){
for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
- fprintf(fh,"%.17e %.17e %.17e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z );
+ // fprintf(fh,"%.17e %.17e %.17e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z );
+ coordinate_vector[offset]=vesicle->filament_list->poly[i]->vlist->vtx[j]->x;
+ coordinate_vector[offset+1]=vesicle->filament_list->poly[i]->vlist->vtx[j]->y;
+ coordinate_vector[offset+2]=vesicle->filament_list->poly[i]->vlist->vtx[j]->z;
}
}
}
+ printout=ts_compress((char *)coordinate_vector,offset*sizeof(double));
+ fprintf(fh,"%s",printout);
+ free(printout);
- fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
- for(i=0;i<blist->n;i++){
- fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
+
+
+ fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"binary\">");
+ free(int_vector);
+ int_vector=(long *)malloc(((blist->n+monono*polyno+filno*(fonono-1))*2+vesicle->tlist->n*3)*sizeof(long));
+ offset=0;
+ for(i=0;i<blist->n;i++,offset+=2){
+// fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
+ int_vector[offset]=blist->bond[i]->vtx1->idx;
+ int_vector[offset+1]=blist->bond[i]->vtx2->idx;
}
//polymeres
if(poly){
poly_idx=vlist->n;
for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
-// fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx);
- fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+i*monono,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+i*monono);
+ for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++,offset+=2){
+ //fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+i*monono,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+i*monono);
+ int_vector[offset]= vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+i*monono;
+ int_vector[offset+1]=vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+i*monono;
+
}
//grafted bonds
- fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx+vlist->n+i*monono);
+ //fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx+vlist->n+i*monono);
+ int_vector[offset]=vesicle->poly_list->poly[i]->grafted_vtx->idx;
+ int_vector[offset+1]=vesicle->poly_list->poly[i]->vlist->vtx[0]->idx+vlist->n+i*monono;
+ offset+=2;
}
}
@@ -441,32 +503,62 @@
if(fil){
poly_idx=vlist->n+monono*polyno;
for(i=0;i<vesicle->filament_list->n;i++){
- for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
- fprintf(fh,"%u %u\n", vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+monono*polyno+i*fonono,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+monono*polyno+i*fonono);
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++,offset+=2){
+// fprintf(fh,"%u %u\n", vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+monono*polyno+i*fonono,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+monono*polyno+i*fonono);
+ int_vector[offset]=vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+monono*polyno+i*fonono;
+ int_vector[offset+1]=vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+monono*polyno+i*fonono;
// fprintf(stderr,"was here\n");
}
}
}
- for(i=0;i<vesicle->tlist->n;i++){
- fprintf(fh,"%u %u %u\n", vesicle->tlist->tria[i]->vertex[0]->idx, vesicle->tlist->tria[i]->vertex[1]->idx, vesicle->tlist->tria[i]->vertex[2]->idx);
+ for(i=0;i<vesicle->tlist->n;i++,offset+=3){
+// fprintf(fh,"%u %u %u\n", vesicle->tlist->tria[i]->vertex[0]->idx, vesicle->tlist->tria[i]->vertex[1]->idx, vesicle->tlist->tria[i]->vertex[2]->idx);
+ int_vector[offset]=vesicle->tlist->tria[i]->vertex[0]->idx;
+ int_vector[offset+1]=vesicle->tlist->tria[i]->vertex[1]->idx;
+ int_vector[offset+2]=vesicle->tlist->tria[i]->vertex[2]->idx;
+
}
- fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
- for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2){
- fprintf(fh,"%u ",i);
+ printout=ts_compress((char *)int_vector,offset*sizeof(long));
+ fprintf(fh,"%s",printout);
+ free(printout);
+
+
+ fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"binary\">");
+ offset=0;
+ for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2,offset++){
+// fprintf(fh,"%u ",i);
+ int_vector[offset]=i;
}
- for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3){ //let's continue counting from where we left of
- fprintf(fh,"%u ", j);
+ for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3,offset++){ //let's continue counting from where we left of
+// fprintf(fh,"%u ", j);
+ int_vector[offset]=j;
}
- fprintf(fh,"\n");
- fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
- for (i=0;i<blist->n+monono*polyno+(fonono-1)*filno;i++){
- fprintf(fh,"3 ");
+// fprintf(fh,"\n");
+ printout=ts_compress((char *)int_vector,offset*sizeof(long));
+ fprintf(fh,"%s",printout);
+ free(printout);
+ fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"binary\">\n");
+ free(int_vector);
+ free(float_vector);
+ free(float_cell_vector);
+ free(coordinate_vector);
+ unsigned char *char_vector=(unsigned char *)malloc((blist->n+monono*polyno+filno*(fonono-1)+vesicle->tlist->n)*sizeof(char));
+ offset=0;
+ for (i=0;i<blist->n+monono*polyno+(fonono-1)*filno;i++,offset++){
+ //fprintf(fh,"3 ");
+ char_vector[offset]=3;
}
- for(i=0;i<vesicle->tlist->n;i++){
- fprintf(fh,"5 ");
+ for(i=0;i<vesicle->tlist->n;i++,offset++){
+ // fprintf(fh,"5 ");
+ char_vector[offset]=5;
}
+ printout=ts_compress((char *)char_vector,offset*sizeof(char));
+ fprintf(fh,"%s",printout);
+ free(printout);
+ free(char_vector);
+
fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
fclose(fh);
return TS_SUCCESS;
diff --git a/src/snapshot.c b/src/snapshot.c
index 53bca9d..3a4de89 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -173,19 +173,27 @@
return nbase;
}
-char *ts_compress(char *data, ts_uint data_len, ts_uint original_len){
+char *ts_compress(char *data, ts_uint data_len){
size_t nbase1, nbase2;
- char *compr;
- size_t number_of_compressed_bytes=ts_compress_data(data, data_len, &compr);
+ unsigned char *compr=(unsigned char *)malloc(data_len);
+ size_t number_of_compressed_bytes=data_len;
+
+ compress(compr,&number_of_compressed_bytes, (unsigned char *)data, data_len);
+// printf("Compressdion error code=%d, Z_OK=%d, Z_BUF_ERROR=%d", errcode, Z_OK, Z_BUF_ERROR);
+
char *encoded_compressed=base64_encode((unsigned char *)compr,number_of_compressed_bytes,&nbase1);
+
free(compr);
- ts_uint header[4]={1, original_len, original_len, number_of_compressed_bytes};
+
+ ts_uint header[4]={1, data_len, data_len, number_of_compressed_bytes};
+
char *encoded_header=(char *)base64_encode((unsigned char *)header, 4*sizeof(ts_uint), &nbase2);
char *return_value=malloc((nbase1+nbase2+1)*sizeof(char));
strncpy(return_value,encoded_header,nbase2);
strncpy(return_value+nbase2,encoded_compressed,nbase1);
*(return_value+nbase1+nbase2)=0;
- printf("Compressed size in bytes= %ld, size of encoded header= %ld, size of encoded compressed= %ld.\n",number_of_compressed_bytes, nbase2, nbase1);
+
+// printf("Compressed size in bytes= %ld, size of encoded header= %ld, size of encoded compressed= %ld.\n",number_of_compressed_bytes, nbase2, nbase1);
free(encoded_compressed);
free(encoded_header);
return return_value;
diff --git a/src/snapshot.h b/src/snapshot.h
index e7a3865..452202e 100644
--- a/src/snapshot.h
+++ b/src/snapshot.h
@@ -26,5 +26,5 @@
void build_decoding_table();
void base64_cleanup();
ts_uint ts_compress_string64(char *data, ts_uint data_len, char **compressed);
-char *ts_compress(char *data, ts_uint data_len, ts_uint original_len);
+char *ts_compress(char *data, ts_uint data_len);
#endif
--
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