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modify exafelSZ.c and exafelSZ.h
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@disheng222
disheng222 committed Jan 16, 2021
1 parent faef189 commit cd21815
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Showing 3 changed files with 127 additions and 44 deletions.
2 changes: 1 addition & 1 deletion sz/include/defines.h
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
#define SZ_VER_MAJOR 2
#define SZ_VER_MINOR 1
#define SZ_VER_BUILD 11
#define SZ_VER_REVISION 0
#define SZ_VER_REVISION 1

#define PASTRI 103
#define HZ 102 //deprecated
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9 changes: 7 additions & 2 deletions sz/include/exafelSZ.h
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Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,20 @@ extern "C" {
#include <stdlib.h>

typedef struct exafelSZ_params{
uint8_t *peaks;
//uint8_t *peaks;
uint16_t *peaksSegs;
uint16_t *peaksRows;
uint16_t *peaksCols;
uint64_t numPeaks;

uint8_t *calibPanel;

uint8_t binSize; //Binning: (pr->binSize x pr->binSize) to (1 x 1)
double tolerance; //SZ pr->tolerance
uint8_t szDim; //1D/2D/3D compression/decompression
//uint8_t szBlockSize; //Currently unused
uint8_t peakSize; //MUST BE ODD AND NOT EVEN! Each peak will have size of: (peakSize x peakSize)

// uint64_t nEvents;
// uint64_t panels;
// uint64_t rows;
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160 changes: 119 additions & 41 deletions sz/src/exafelSZ.c
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Original file line number Diff line number Diff line change
Expand Up @@ -38,14 +38,29 @@ void exafelSZ_params_checkDecomp(exafelSZ_params*pr, size_t panels, size_t rows,
}

void exafelSZ_params_checkComp(exafelSZ_params*pr, size_t panels, size_t rows, size_t cols){
if(pr->peaks==NULL){
printf("ERROR: peaks is NULL : peaks=%ld\n",(long)pr->peaks);
if(pr->peaksSegs==NULL || pr->peaksRows==NULL || pr->peaksCols==NULL){
printf("ERROR: One or more of the following are NULL : peaksSegs , peaksRows , peaksCols\n");
assert(0);
}
exafelSZ_params_checkDecomp(pr, panels, rows, cols);
}

void exafelSZ_params_print(){
void exafelSZ_params_print(exafelSZ_params*pr){
printf("Configuration (exafelSZ_params) :\n");
printf("binSize: %d\n",pr->binSize);
printf("tolerance:%e\n",pr->tolerance);
printf("szDim:%d\n",pr->szDim);
printf("peakSize:%d\n",pr->peakSize);
//printf("nEvents:%d\n",pr->nEvents);
//printf("panels:%d\n",pr->panels);
//printf("rows:%d\n",pr->rows);
//printf("cols:%d\n",pr->cols);
printf("\n");
printf("CALCULATED VARIABLES\n");
printf("binnedRows:%d\n",pr->binnedRows);
printf("binnedCols:%d\n",pr->binnedCols);
printf("peakRadius:%d\n",pr->peakRadius);
printf("\n");
// outs<<"Configuration (exafelSZ_params) : "<<endl;
// outs<<"SMOOTHING: NO"<<" (ROI and RONI are NOT replaced by local avg values)"<<endl;
// outs<<"binSize:"<<binSize<<endl;
Expand Down Expand Up @@ -81,66 +96,103 @@ static inline size_t calcIdx_2D(int i1, int i0, int size0){

unsigned char * exafelSZ_Compress(void* _pr,
void* _origData,
size_t nEvents, size_t panels, size_t rows, size_t cols,
size_t r4, size_t r3, size_t r2, size_t r1,
size_t *compressedSize)
{
//printf("COMPRESS\n"); *compressedSize=0; return NULL;
size_t nEvents,panels,rows,cols;
if(r4==0)
nEvents=1;
else
nEvents=r4;
panels=r1;
rows=r2;
cols=r3;
//printf("AMG : exafelSZ_Compress : nEvents,panels,rows,cols = %d , %d , %d , %d\n",nEvents,panels,rows,cols);

float *origData=(float*)_origData;
exafelSZ_params *pr=(exafelSZ_params*)_pr;

exafelSZ_params_process(pr, panels, rows, cols);
exafelSZ_params_checkDecomp(pr, panels, rows, cols);

exafelSZ_params *pr=(exafelSZ_params*)_pr;

exafelSZ_params_process(pr, panels, rows, cols);
exafelSZ_params_checkComp(pr, panels, rows, cols);
//exafelSZ_params_print(pr);

uint8_t *roiM=(uint8_t*)malloc(nEvents*panels*rows*cols) ;
float *roiData=(float*)malloc(nEvents*panels*rows*cols*sizeof(float)) ;
float *binnedData=(float*)malloc(nEvents*panels*pr->binnedRows*pr->binnedCols*sizeof(float)) ;
//float *binnedData=(float*)malloc(nEvents*panels*rows*cols*sizeof(float)) ;

size_t e,p,r,c,pk,ri,ci,br,bc,roii,bi;

/*
printf("AMG : exafelSZ_Compress : pr->numPeaks = %d\n",pr->numPeaks);
printf("S:\n");
for(e=0;e<pr->numPeaks;e++)
printf("%d ",pr->peaksSegs[e]);
printf("\nR:\n");
for(e=0;e<pr->numPeaks;e++)
printf("%d ",pr->peaksRows[e]);
printf("\nC:\n");
for(e=0;e<pr->numPeaks;e++)
printf("%d ",pr->peaksCols[e]);
printf("\n");
*/

//Generate the ROI mask: NOTE: 0 means affirmative in ROI mask! This comes from the python scripts!
//First, initialize with calibration panel:
for(e=0;e<nEvents;e++){ //Event
for(p=0;p<panels;p++){ //Panel
for(r=0;r<rows;r++){ //Row
for(c=0;c<cols;c++){ //Column
roiM[calcIdx_4D(e,p,r,c,panels,rows,cols)]=pr->calibPanel[calcIdx_2D(r,c,cols)];
//roiM[calcIdx_4D(e,p,r,c,panels,rows,cols)]=pr->calibPanel[calcIdx_2D(r,c,cols)]; //calibPanel is a single segment copied over all the event(image)
roiM[calcIdx_4D(e,p,r,c,panels,rows,cols)]=pr->calibPanel[calcIdx_3D(p,r,c,rows,cols)]; //calibPanel is as big as the event(image) itself
}
}
}
}
uint64_t peaksBytePos=0; //Position in the peaks buffer
//uint64_t peaksBytePos=0; //Position in the peaks buffer
//Now process the peaks and generate the mask:
uint64_t nPeaksTotal=0; //Total number of peaks
for(e=0;e<nEvents;e++){ //Event
uint64_t nPeaks=*(uint64_t*)(&pr->peaks[peaksBytePos]);
peaksBytePos+=8;
//uint64_t nPeaks=*(uint64_t*)(&pr->peaks[peaksBytePos]);
//peaksBytePos+=8;

//peaksBytePos+=8;//Skip the second one! This is due to the problem in Python.

nPeaksTotal+=nPeaks;
for(pk=0;pk<nPeaks;pk++){
uint16_t p_=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Panel for the current peak
peaksBytePos+=2;
uint16_t r_=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Row for the current peak
peaksBytePos+=2;
uint16_t c_=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Col for the current peak
peaksBytePos+=2;
nPeaksTotal+=pr->numPeaks;
for(pk=0;pk<pr->numPeaks;pk++){
//uint16_t p_=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Panel for the current peak
//peaksBytePos+=2;
//uint16_t r_=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Row for the current peak
//peaksBytePos+=2;
//uint16_t c_=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Col for the current peak
//peaksBytePos+=2;

uint16_t p_=pr->peaksSegs[pk];
uint16_t r_=pr->peaksRows[pk];
uint16_t c_=pr->peaksCols[pk];

if(p_>=panels){
printf("ERROR: Peak coordinate out of bounds: Panel=%d, Valid range: 0,%d\n",(int)p_,(int)panels-1);
assert(0);
printf("Skipping this peak...\n");
continue;
}
if(r_>=rows){
printf("ERROR: Peak coordinate out of bounds: Row=%d, Valid range: 0,%d\n",(int)r_,(int)rows-1);
assert(0);
printf("Skipping this peak...\n");
continue;
}
if(c_>=cols){
printf("ERROR: Peak coordinate out of bounds: Col=%d, Valid range: 0,%d\n",(int)c_,(int)cols-1);
assert(0);
printf("Skipping this peak...\n");
continue;
}

for(ri=r_-pr->peakRadius;ri<=r_+pr->peakRadius;ri++){ //ri: row index. Just a temporary variable.
for(ci=c_-pr->peakRadius;ci<=c_+pr->peakRadius;ci++){ //ci: column index. Just a temporary variable.
if(ri<rows && ci<cols){ //Check whether inside bounds or not
if(ri<rows && ci<cols){ //Check whether inside the bounds or not
roiM[calcIdx_4D(e,p_,ri,ci,panels,rows,cols)]=0;
}
}
Expand Down Expand Up @@ -256,24 +308,33 @@ unsigned char * exafelSZ_Compress(void* _pr,
//printf("nPeaksTotal=%d\n",nPeaksTotal);
//printf("bytePos=%d\n",bytePos);

peaksBytePos=0;
//peaksBytePos=0;
for(e=0;e<nEvents;e++){
uint64_t nPeaks=*(uint64_t*)(&pr->peaks[peaksBytePos]);
peaksBytePos+=8;
//peaksBytePos+=8;//Skip the second one. This is due to the error in Python!
//uint64_t nPeaks=*(uint64_t*)(&pr->peaks[peaksBytePos]);
//peaksBytePos+=8;
////peaksBytePos+=8;//Skip the second one. This is due to the error in Python!

*(uint64_t*)(&compressedBuffer[bytePos])=nPeaks;
//*(uint64_t*)(&compressedBuffer[bytePos])=nPeaks;
*(uint64_t*)(&compressedBuffer[bytePos])=pr->numPeaks;
bytePos+=8;
for(pk=0;pk<nPeaks;pk++){
*(uint16_t*)(&compressedBuffer[bytePos])=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Panel for the current peak
//for(pk=0;pk<nPeaks;pk++){
for(pk=0;pk<pr->numPeaks;pk++){
//*(uint16_t*)(&compressedBuffer[bytePos])=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Panel for the current peak
//bytePos+=2;
//peaksBytePos+=2;
//*(uint16_t*)(&compressedBuffer[bytePos])=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Row for the current peak
//bytePos+=2;
//peaksBytePos+=2;
//*(uint16_t*)(&compressedBuffer[bytePos])=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Column for the current peak
//bytePos+=2;
//peaksBytePos+=2;

*(uint16_t*)(&compressedBuffer[bytePos])=pr->peaksSegs[pk]; //Panel for the current peak
bytePos+=2;
peaksBytePos+=2;
*(uint16_t*)(&compressedBuffer[bytePos])=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Row for the current peak
*(uint16_t*)(&compressedBuffer[bytePos])=pr->peaksRows[pk]; //Row for the current peak
bytePos+=2;
peaksBytePos+=2;
*(uint16_t*)(&compressedBuffer[bytePos])=*(uint16_t*)(&pr->peaks[peaksBytePos]); //Column for the current peak
*(uint16_t*)(&compressedBuffer[bytePos])=pr->peaksCols[pk]; //Column for the current peak
bytePos+=2;
peaksBytePos+=2;
}
}
// cout<<"peaks"<<endl;
Expand Down Expand Up @@ -329,9 +390,20 @@ unsigned char * exafelSZ_Compress(void* _pr,

void* exafelSZ_Decompress(void *_pr,
unsigned char*_compressedBuffer,
size_t nEvents, size_t panels, size_t rows, size_t cols,
size_t r4, size_t r3, size_t r2, size_t r1,
size_t compressedSize)
{
size_t nEvents,panels,rows,cols;
if(r4==0)
nEvents=1;
else
nEvents=r4;
panels=r1;
rows=r2;
cols=r3;
//printf("AMG : exafelSZ_Decompress : nEvents,panels,rows,cols = %d , %d , %d , %d\n",nEvents,panels,rows,cols);

//printf("DECOMPRESS\n");return NULL;
uint8_t *compressedBuffer=(uint8_t *)_compressedBuffer;
exafelSZ_params *pr=(exafelSZ_params *)_pr;
exafelSZ_params_process(pr, panels, rows, cols);
Expand All @@ -342,7 +414,6 @@ void* exafelSZ_Decompress(void *_pr,
uint8_t *roiM=(uint8_t*)malloc(nEvents*panels*rows*cols);
size_t e,p,r,c,pk,ri,ci,br,bc;


/*
Compressed Data Layout:
nPeaksTotal : 8 bytes : (1 x uint64_t)
Expand Down Expand Up @@ -418,7 +489,8 @@ void* exafelSZ_Decompress(void *_pr,
printf("ERROR: calcIdx_4D(e,p,r,c,panels,rows,cols) = calcIdx_4D(%d,%d,%d,%d,%d,%d,%d) = %d",(int)e,(int)p,(int)r,(int)c,(int)panels,(int)rows,(int)cols,(int)calcIdx_4D(e,p,r,c,panels,rows,cols));
assert(0);
}
roiM[calcIdx_4D(e,p,r,c,panels,rows,cols)]=pr->calibPanel[calcIdx_2D(r,c,cols)];
//roiM[calcIdx_4D(e,p,r,c,panels,rows,cols)]=pr->calibPanel[calcIdx_2D(r,c,cols)]; //calibPanel is a single segment copied over all the event(image)
roiM[calcIdx_4D(e,p,r,c,panels,rows,cols)]=pr->calibPanel[calcIdx_3D(p,r,c,rows,cols)]; //calibPanel is as big as the event(image) itself
}
}
}
Expand All @@ -437,17 +509,23 @@ void* exafelSZ_Decompress(void *_pr,
uint16_t c_=*(uint16_t*)(&peaks[peaksBytePos]); //Col for the current peak
peaksBytePos+=2;

if(p_<0 || p_>=panels){
if(p_>=panels){
printf("ERROR: Peak coordinate out of bounds: Panel=%d, Valid range: 0,%d\n",(int)p_,(int)panels-1);
assert(0);
printf("Skipping this peak...\n");
continue;
}
if(r_<0 || r_>=rows){
if(r_>=rows){
printf("ERROR: Peak coordinate out of bounds: Row=%d, Valid range: 0,%d\n",(int)r_,(int)rows-1);
assert(0);
printf("Skipping this peak...\n");
continue;
}
if(c_<0 || c_>=cols){
if(c_>=cols){
printf("ERROR: Peak coordinate out of bounds: Col=%d, Valid range: 0,%d\n",(int)c_,(int)cols-1);
assert(0);
printf("Skipping this peak...\n");
continue;
}

for(ri=r_-pr->peakRadius;ri<=r_+pr->peakRadius;ri++){ //ri: row index. Just a temporary variable.
Expand Down

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