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Made the reader faster for 2D Uncompressed images
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@MattHazard
MattHazard committed Dec 10, 2024
1 parent 9cd6495 commit 6fb4d97
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Showing 3 changed files with 101 additions and 105 deletions.
8 changes: 4 additions & 4 deletions mexSrc/parallelwritetiffmex.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -30,17 +30,17 @@ void mexFunction(int nlhs, mxArray *plhs[],
if(mxIsEmpty(prhs[1])) mexErrMsgIdAndTxt("tiff:inputError","All input data axes must be of at least size 1");

std::string compression = "lzw";
if(nrhs == 3){
if(!mxIsClass(prhs[2], "string")){
if(!mxIsChar(prhs[2])) mexErrMsgIdAndTxt("tiff:inputError","The third argument must be a string");
if(nrhs == 4){
if(!mxIsClass(prhs[3], "string")){
if(!mxIsChar(prhs[3])) mexErrMsgIdAndTxt("tiff:inputError","The fourth argument must be a string");
compression = mxArrayToString(prhs[0]);
}
else{
mxArray* mString[1];
mxArray* mCharA[1];

// Convert string to char array
mString[0] = mxDuplicateArray(prhs[2]);
mString[0] = mxDuplicateArray(prhs[3]);
mexCallMATLAB(1, mCharA, 1, mString, "char");
compression = mxArrayToString(mCharA[0]);
}
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2 changes: 1 addition & 1 deletion python/setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ def run(self):
# Packaging for PyPI
setup(
name="cpp-tiff",
version="1.0.8",
version="1.0.9",
description="Python wrappers for cpp-tiff",
url='https://github.com/abcucberkeley/cpp-tiff',
author='Matthew Mueller',
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196 changes: 96 additions & 100 deletions src/parallelreadtiff.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -283,104 +283,103 @@ uint8_t readTiffParallel2D(uint64_t x, uint64_t y, uint64_t z, const char* fileN

// The other method won't work on specific slices of 3D images for now
// so start slice must also be 0
if(compressed > 1 || startSlice){
TIFFClose(tif);
#pragma omp parallel for
for(w = 0; w < numWorkers; w++){

uint8_t outCounter = 0;
TIFF* tif = TIFFOpen(fileName, "r");
while(!tif){
tif = TIFFOpen(fileName, "r");
if(outCounter == 3){
#pragma omp critical
{
err = 1;
sprintf(errString,"Thread %d: File \"%s\" cannot be opened\n",w,fileName);
if(numWorkers > 1 || compressed > 1){
#pragma omp parallel for
for(w = 0; w < numWorkers; w++){

uint8_t outCounter = 0;
TIFF* tif = TIFFOpen(fileName, "r");
while(!tif){
tif = TIFFOpen(fileName, "r");
if(outCounter == 3){
#pragma omp critical
{
err = 1;
sprintf(errString,"Thread %d: File \"%s\" cannot be opened\n",w,fileName);
}
continue;
}
continue;
outCounter++;
}
outCounter++;
}

void* buffer = malloc(x*stripSize*bytes);


uint8_t counter = 0;
while(!TIFFSetDirectory(tif, startSlice) && counter<3){
printf("Thread %d: File \"%s\" Directory \"%d\" failed to open. Try %d\n",w,fileName,0,counter+1);
counter++;
if(counter == 3){
#pragma omp critical
{
err = 1;
sprintf(errString,"Thread %d: File \"%s\" cannot be opened\n",w,fileName);

void* buffer = malloc(x*stripSize*bytes);


uint8_t counter = 0;
while(!TIFFSetDirectory(tif, startSlice) && counter<3){
printf("Thread %d: File \"%s\" Directory \"%d\" failed to open. Try %d\n",w,fileName,0,counter+1);
counter++;
if(counter == 3){
#pragma omp critical
{
err = 1;
sprintf(errString,"Thread %d: File \"%s\" cannot be opened\n",w,fileName);
}
}
}
}
for (int64_t i = (w*batchSize); i < (w+1)*batchSize; i++)
{
if(i*stripSize >= y || err) break;
//loading the data into a buffer
int64_t cBytes = TIFFReadEncodedStrip(tif, i, buffer, stripSize*x*bytes);
if(cBytes < 0){
#pragma omp critical
{
//errBak = 1;
err = 1;
sprintf(errString,"Thread %d: Strip %ld cannot be read\n",w,i);
for (int64_t i = (w*batchSize); i < (w+1)*batchSize; i++)
{
if(i*stripSize >= y || err) break;
//loading the data into a buffer
int64_t cBytes = TIFFReadEncodedStrip(tif, i, buffer, stripSize*x*bytes);
if(cBytes < 0){
#pragma omp critical
{
//errBak = 1;
err = 1;
sprintf(errString,"Thread %d: Strip %ld cannot be read\n",w,i);
}
break;
}
break;
}
if(!flipXY){
memcpy(tiff+((i*stripSize*x)*bytes),buffer,cBytes);
continue;
}
switch(bits){
case 8:
// Map Values to flip x and y for MATLAB
for(int64_t k = 0; k < stripSize; k++){
if((k+(i*stripSize)) >= y) break;
for(int64_t j = 0; j < x; j++){
((uint8_t*)tiff)[((j*y)+(k+(i*stripSize)))] = ((uint8_t*)buffer)[j+(k*x)];
if(!flipXY){
memcpy(tiff+((i*stripSize*x)*bytes),buffer,cBytes);
continue;
}
switch(bits){
case 8:
// Map Values to flip x and y for MATLAB
for(int64_t k = 0; k < stripSize; k++){
if((k+(i*stripSize)) >= y) break;
for(int64_t j = 0; j < x; j++){
((uint8_t*)tiff)[((j*y)+(k+(i*stripSize)))] = ((uint8_t*)buffer)[j+(k*x)];
}
}
}
break;
case 16:
// Map Values to flip x and y for MATLAB
for(int64_t k = 0; k < stripSize; k++){
if((k+(i*stripSize)) >= y) break;
for(int64_t j = 0; j < x; j++){
((uint16_t*)tiff)[((j*y)+(k+(i*stripSize)))] = ((uint16_t*)buffer)[j+(k*x)];
break;
case 16:
// Map Values to flip x and y for MATLAB
for(int64_t k = 0; k < stripSize; k++){
if((k+(i*stripSize)) >= y) break;
for(int64_t j = 0; j < x; j++){
((uint16_t*)tiff)[((j*y)+(k+(i*stripSize)))] = ((uint16_t*)buffer)[j+(k*x)];
}
}
}
break;
case 32:
// Map Values to flip x and y for MATLAB
for(int64_t k = 0; k < stripSize; k++){
if((k+(i*stripSize)) >= y) break;
for(int64_t j = 0; j < x; j++){
((float*)tiff)[((j*y)+(k+(i*stripSize)))] = ((float*)buffer)[j+(k*x)];
break;
case 32:
// Map Values to flip x and y for MATLAB
for(int64_t k = 0; k < stripSize; k++){
if((k+(i*stripSize)) >= y) break;
for(int64_t j = 0; j < x; j++){
((float*)tiff)[((j*y)+(k+(i*stripSize)))] = ((float*)buffer)[j+(k*x)];
}
}
}
break;
case 64:
// Map Values to flip x and y for MATLAB
for(int64_t k = 0; k < stripSize; k++){
if((k+(i*stripSize)) >= y) break;
for(int64_t j = 0; j < x; j++){
((double*)tiff)[((j*y)+(k+(i*stripSize)))] = ((double*)buffer)[j+(k*x)];
break;
case 64:
// Map Values to flip x and y for MATLAB
for(int64_t k = 0; k < stripSize; k++){
if((k+(i*stripSize)) >= y) break;
for(int64_t j = 0; j < x; j++){
((double*)tiff)[((j*y)+(k+(i*stripSize)))] = ((double*)buffer)[j+(k*x)];
}
}
}
break;
break;
}
}
free(buffer);
TIFFClose(tif);
}
free(buffer);
TIFFClose(tif);
}
}
else{
uint64_t stripsPerDir = (uint64_t)ceil((double)y/(double)stripSize);
void* tiffC = NULL;
FILE *fp = fopen(fileName, "rb");
if(!fp){
printf("File \"%s\" cannot be opened from Disk\n",fileName);
Expand All @@ -397,32 +396,29 @@ uint8_t readTiffParallel2D(uint64_t x, uint64_t y, uint64_t z, const char* fileN
uint64_t offset = 0;
uint64_t* offsets = NULL;
TIFFGetField(tif, TIFFTAG_STRIPOFFSETS, &offsets);
uint64_t* byteCounts = NULL;
TIFFGetField(tif, TIFFTAG_STRIPBYTECOUNTS, &byteCounts);
if(!offsets || !byteCounts){
printf("Could not get offsets or byte counts from the tiff file\n");
if(!offsets){
printf("Could not get offsets from the tiff file\n");
err = 1;
return err;
}
offset = offsets[0];
uint64_t fOffset = offsets[stripsPerDir-1]+byteCounts[stripsPerDir-1];
uint64_t zSize = x*y*bytes;
TIFFSetDirectory(tif,1);
TIFFGetField(tif, TIFFTAG_STRIPOFFSETS, &offsets);
uint64_t gap = offsets[0]-fOffset;

fseek(fp, offset, SEEK_SET);


TIFFClose(tif);

size_t bytesRead = fread(tiff, 1, zSize, fp);
fclose(fp);
if(flipXY){

if(!flipXY){
fread(tiff, 1, zSize, fp);
}
else{
uint64_t size = x*y*z*(bits/8);
void* tiffC = malloc(size);
memcpy(tiffC,tiff,size);
#pragma omp parallel for
tiffC = malloc(size);
fread(tiffC, 1, zSize, fp);
}
fclose(fp);
if(flipXY){
for(uint64_t k = 0; k < z; k++){
for(uint64_t j = 0; j < x; j++){
for(uint64_t i = 0; i < y; i++){
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