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Removed the alternative reading method for uncompressed 3D tiffs
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@MattHazard
MattHazard committed Dec 4, 2024
1 parent 41ae782 commit 9cd6495
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Showing 2 changed files with 76 additions and 149 deletions.
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="1.0.7",
version="1.0.8",
description="Python wrappers for cpp-tiff",
url='https://github.com/abcucberkeley/cpp-tiff',
author='Matthew Mueller',
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223 changes: 75 additions & 148 deletions src/parallelreadtiff.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -85,177 +85,104 @@ uint8_t readTiffParallel(uint64_t x, uint64_t y, uint64_t z, const char* fileNam
int32_t batchSize = (z-1)/numWorkers+1;
uint64_t bytes = bits/8;

uint16_t compressed = 1;
TIFF* tif = TIFFOpen(fileName, "r");
TIFFGetField(tif, TIFFTAG_COMPRESSION, &compressed);



int32_t w;
uint8_t errBak = 0;
uint8_t err = 0;
char errString[10000];
if(compressed > 1 || z < 32768){
TIFFClose(tif);
#pragma omp parallel for
for(w = 0; w < numWorkers; w++){
#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){
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;
}
outCounter++;
}

void* buffer = malloc(x*stripSize*bytes);
for(int64_t dir = startSlice+(w*batchSize); dir < startSlice+((w+1)*batchSize); dir++){
if(dir>=z+startSlice || err) break;

uint8_t counter = 0;
while(!TIFFSetDirectory(tif, (uint64_t)dir) && counter<3){
counter++;
if(counter == 3){
#pragma omp critical
{
err = 1;
sprintf(errString,"Thread %d: File \"%s\" cannot be opened\n",w,fileName);
}
continue;
}
outCounter++;
}
if(err) break;
for (int64_t i = 0; i*stripSize < y; i++)
{

void* buffer = malloc(x*stripSize*bytes);
for(int64_t dir = startSlice+(w*batchSize); dir < startSlice+((w+1)*batchSize); dir++){
if(dir>=z+startSlice || err) break;

uint8_t counter = 0;
while(!TIFFSetDirectory(tif, (uint64_t)dir) && counter<3){
counter++;
if(counter == 3){
#pragma omp critical
{
err = 1;
sprintf(errString,"Thread %d: File \"%s\" cannot be opened\n",w,fileName);
}
//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;
}
if(err) break;
for (int64_t i = 0; i*stripSize < y; i++)
{

//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;
}
if(!flipXY){
memcpy(tiff+(((i*stripSize*x)+((dir-startSlice)*(x*y)))*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)))+((dir-startSlice)*(x*y))] = ((uint8_t*)buffer)[j+(k*x)];
}
if(!flipXY){
memcpy(tiff+(((i*stripSize*x)+((dir-startSlice)*(x*y)))*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)))+((dir-startSlice)*(x*y))] = ((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)))+((dir-startSlice)*(x*y))] = ((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)))+((dir-startSlice)*(x*y))] = ((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)))+((dir-startSlice)*(x*y))] = ((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)))+((dir-startSlice)*(x*y))] = ((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)))+((dir-startSlice)*(x*y))] = ((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)))+((dir-startSlice)*(x*y))] = ((double*)buffer)[j+(k*x)];
}
break;
}
}
break;
}
}
free(buffer);
TIFFClose(tif);
}
}
else{
uint64_t stripsPerDir = (uint64_t)ceil((double)y/(double)stripSize);
FILE *fp = fopen(fileName, "rb");
if(!fp) {
printf("File \"%s\" cannot be opened from Disk\n",fileName);
err = 1;
return err;
}

if(!tif){
printf("File \"%s\" cannot be opened\n",fileName);
err = 1;
return err;
}

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");
err = 1;
return err;
}
offset = offsets[0];
uint64_t fOffset = offsets[stripsPerDir-1]+byteCounts[stripsPerDir-1];
uint64_t zSize = fOffset-offset;
TIFFSetDirectory(tif,1);
TIFFGetField(tif, TIFFTAG_STRIPOFFSETS, &offsets);
uint64_t gap = offsets[0]-fOffset;

fseek(fp, offset, SEEK_SET);


free(buffer);
TIFFClose(tif);
size_t bytesRead = fread(tiff, 1, zSize, fp);
fclose(fp);
uint64_t size = x*y*z*(bits/8);
void* tiffC = malloc(size);
memcpy(tiffC,tiff,size);
#pragma omp parallel for
for(uint64_t k = 0; k < z; k++){
for(uint64_t j = 0; j < x; j++){
for(uint64_t i = 0; i < y; i++){
switch(bits){
case 8:
((uint8_t*)tiff)[i+(j*y)+(k*x*y)] = ((uint8_t*)tiffC)[j+(i*x)+(k*x*y)];
break;
case 16:
((uint16_t*)tiff)[i+(j*y)+(k*x*y)] = ((uint16_t*)tiffC)[j+(i*x)+(k*x*y)];
break;
case 32:
((float*)tiff)[i+(j*y)+(k*x*y)] = ((float*)tiffC)[j+(i*x)+(k*x*y)];
break;
case 64:
((double*)tiff)[i+(j*y)+(k*x*y)] = ((double*)tiffC)[j+(i*x)+(k*x*y)];
break;
}
}
}
}
free(tiffC);
}
if(err){
if(errBak) return readTiffParallelBak(x, y, z, fileName, tiff, bits, startSlice, flipXY);
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