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Enable tiff reader to read tiff from a stack with user specified step size #9

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f3abdbf
Updates to enable reading with steps.
Jun 6, 2025
ef56e07
Update parallelreadtiff.cpp
xs254 Jun 6, 2025
18db8ef
Merge pull request #1 from xs254/stepread_v1
xs254 Jun 6, 2025
7eb69b9
Update tests.m
xs254 Jun 6, 2025
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2 changes: 2 additions & 0 deletions CMakeLists.txt
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Expand Up @@ -45,6 +45,8 @@ set(ZSTD_DIR "${CMAKE_CURRENT_SOURCE_DIR}/dependencies/${ZSTD_VER}")
add_subdirectory(${ZSTD_DIR}/build/cmake)
set_property(TARGET libzstd_static PROPERTY POSITION_INDEPENDENT_CODE ON)

# Added by XS, add zlib for compilation to work
include_directories(${CMAKE_BINARY_DIR}/dependencies/zlib-1.2.8)
# Add libtiff
include_directories(${CMAKE_BINARY_DIR}/dependencies/${TIFF_VER}/libtiff)
include_directories(${ZSTD_DIR}/lib)
Expand Down
18 changes: 15 additions & 3 deletions mexSrc/compile_parallelReadTiff.m
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Expand Up @@ -54,10 +54,22 @@
system('chmod 777 ../macArm/parallelReadTiff.mexmaca64');
end
elseif ispc
setenv('MW_MINGW64_LOC','C:/mingw64');
releaseFolder = '../windows';
%setenv('MW_MINGW64_LOC','C:/mingw64');
releaseFolder = '..\windows';
if ~exist(releaseFolder, 'dir')
mkdir(releaseFolder);
end
mex -outdir ../windows -output parallelReadTiff.mexw64 -v CXX="C:/mingw64/bin/g++" -v CXXOPTIMFLAGS="-DNDEBUG -O3" LDOPTIMFLAGS="-Wl',-rpath='''$ORIGIN'''' -O3 -DNDEBUG" CXXFLAGS='$CXXFLAGS -fopenmp -O3' LDFLAGS='$LDFLAGS -fopenmp -O3' -I'C:/Users/matt/Documents/GitHub/c-tiff/jenkinsBuild/install/include' -L'C:/Users/matt/Documents/GitHub/c-tiff/jenkinsBuild/install/lib' -lcppTiff.dll parallelreadtiffmex.cpp
mex -outdir ..\windows -output parallelReadTiff.mexw64 ...
-v CXX="C:\ProgramData\MATLAB\SupportPackages\R2022b\3P.instrset\mingw_w64.instrset\bin\g++" -v CXXOPTIMFLAGS="-DNDEBUG -O3" ...
LDOPTIMFLAGS="-Wl',-rpath='''$ORIGIN'''' -O3 -DNDEBUG" ...
CXXFLAGS='$CXXFLAGS -fopenmp -O3' LDFLAGS='$LDFLAGS -fopenmp -O3' ...
-I'..\dependencies\libdeflate-1.18' ...
-I'..\dependencies\tiff-4.7.0' ...
-I'..\dependencies\tiff-4.7.0\libtiff' ...
-I'..\build\dependencies\tiff-4.7.0\libtiff' ...
-I'..\dependencies\zlib-1.2.8' ...
-I'..\dependencies\zstd-1.5.6' ...
-I'..\build\dependencies\zlib-1.2.8' ...
-L'..\build' -lcppTiff.dll ...
parallelreadtiffmex.cpp
end
38 changes: 27 additions & 11 deletions mexSrc/parallelreadtiffmex.cpp
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Expand Up @@ -5,7 +5,8 @@
#include "../src/helperfunctions.h"
#include "../src/parallelreadtiff.h"


// Modified to read tiff from stack with a step size by accepting [start step end] as second argument.
// *Read with step is only enabled for the case of 3D, imageJ and 2D case are not touched.
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
Expand Down Expand Up @@ -44,7 +45,7 @@ void mexFunction(int nlhs, mxArray *plhs[],
TIFF* tif = TIFFOpen(fileName, "r");
if(!tif) mexErrMsgIdAndTxt("tiff:inputError","File \"%s\" cannot be opened",fileName);

uint64_t x = 1,y = 1,z = 1,bits = 1, startSlice = 0;
uint64_t x = 1,y = 1,z = 1,bits = 1, startSlice = 0, sliceStep = 1;
TIFFGetField(tif, TIFFTAG_IMAGEWIDTH, &x);
TIFFGetField(tif, TIFFTAG_IMAGELENGTH, &y);

Expand All @@ -58,10 +59,8 @@ void mexFunction(int nlhs, mxArray *plhs[],
}
}
else{
if(mxGetN(prhs[1]) != 2){
mexErrMsgIdAndTxt("tiff:inputError","Input range is not 2");
}
else{
// Modified for accepting both [start end] and [start step end] as second argument
if(mxGetN(prhs[1]) == 2){
startSlice = (uint64_t)*(mxGetPr(prhs[1]))-1;
z = (uint64_t)*((mxGetPr(prhs[1])+1))-startSlice;
uint64_t maxSize = 0;
Expand All @@ -74,6 +73,23 @@ void mexFunction(int nlhs, mxArray *plhs[],
mexErrMsgIdAndTxt("tiff:rangeOutOfBound","Range is out of bounds");
}
}
else if (mxGetN(prhs[1]) == 3){
if(isImageJIm(fileName)){
mexErrMsgIdAndTxt("tiff:inputError","Read with step is not supported for ImageJ.");
}
startSlice = (uint64_t)*(mxGetPr(prhs[1]))-1;
sliceStep = (uint64_t)*((mxGetPr(prhs[1])+1));
uint64_t endSlice = (uint64_t)*((mxGetPr(prhs[1])+2))-1;
z = (endSlice-startSlice)/sliceStep+1;

uint64_t maxSize = getImageSizeZ(fileName);
if (startSlice < 0 || endSlice+1 > maxSize){
mexErrMsgIdAndTxt("tiff:rangeOutOfBound","Range is out of bounds");
}
}
else{
mexErrMsgIdAndTxt("tiff:inputError","Input range is not 2 or 3");
}
}

TIFFGetField(tif, TIFFTAG_BITSPERSAMPLE, &bits);
Expand Down Expand Up @@ -139,27 +155,27 @@ void mexFunction(int nlhs, mxArray *plhs[],
mexErrMsgIdAndTxt("tiff:dataTypeError","Data type not suppported");
}
}
// Case for 3D
// Case for 3D, modified to accept sliceStep as extra argument
else{
if(bits == 8){
plhs[0] = mxCreateNumericArray(3,(mwSize*)dim,mxUINT8_CLASS, mxREAL);
uint8_t* tiff = (uint8_t*)mxGetPr(plhs[0]);
err = readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, stripSize, flipXY);
err = readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, sliceStep, stripSize, flipXY);
}
else if(bits == 16){
plhs[0] = mxCreateNumericArray(3,(mwSize*)dim,mxUINT16_CLASS, mxREAL);
uint16_t* tiff = (uint16_t*)mxGetPr(plhs[0]);
err = readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, stripSize, flipXY);
err = readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, sliceStep, stripSize, flipXY);
}
else if(bits == 32){
plhs[0] = mxCreateNumericArray(3,(mwSize*)dim,mxSINGLE_CLASS, mxREAL);
float* tiff = (float*)mxGetPr(plhs[0]);
err = readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, stripSize, flipXY);
err = readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, sliceStep, stripSize, flipXY);
}
else if(bits == 64){
plhs[0] = mxCreateNumericArray(3,(mwSize*)dim,mxDOUBLE_CLASS, mxREAL);
double* tiff = (double*)mxGetPr(plhs[0]);
err = readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, stripSize, flipXY);
err = readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, sliceStep, stripSize, flipXY);
}
else{
mexErrMsgIdAndTxt("tiff:dataTypeError","Data type not suppported");
Expand Down
21 changes: 17 additions & 4 deletions mexSrc/tests.m
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@@ -1,8 +1,21 @@
addpath('../windows');
im = rand(100,100,100,'single');
im(:,:,2:2:100) = 1;
parallelWriteTiff('test.tif',im);

%%
%% parallelReadTiff in different modes
imT = parallelReadTiff('test.tif');

imT_1_6 = parallelReadTiff('test.tif',[1 6]); %[start end]
imT_1_2_11 = parallelReadTiff('test.tif',[1 2 11]);%[start step end]
imT_2_2_12 = parallelReadTiff('test.tif',[2 2 12]);%[start step end]
%% Visualize tiff read by different modes
figure;
montage(imT_1_6,'Size',[1 6]);
title('1 to 6');
figure;
montage(imT_1_2_11,'Size',[1 6]);
title('1 to 11 at step 2');
figure;
montage(imT_2_2_12,'Size',[1 6]);
title('2 to 12 at step 2');
%%
imSize = getImageSizeMex('test.tif');
imSize = getImageSizeMex('test.tif');
46 changes: 27 additions & 19 deletions src/parallelreadtiff.cpp
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Expand Up @@ -81,7 +81,8 @@ uint8_t readTiffParallelBak(uint64_t x, uint64_t y, uint64_t z, const char* file
return err;
}

uint8_t readTiffParallel(uint64_t x, uint64_t y, uint64_t z, const char* fileName, void* tiff, uint64_t bits, uint64_t startSlice, uint64_t stripSize, uint8_t flipXY){
// Modified such that the function can read tiff from stack with step size as specified by sliceStep.
uint8_t readTiffParallel(uint64_t x, uint64_t y, uint64_t z, const char* fileName, void* tiff, uint64_t bits, uint64_t startSlice, uint64_t sliceStep, uint64_t stripSize, uint8_t flipXY){
int32_t numWorkers = omp_get_max_threads();
int32_t batchSize = (z-1)/numWorkers+1;
uint64_t bytes = bits/8;
Expand Down Expand Up @@ -109,8 +110,10 @@ uint8_t readTiffParallel(uint64_t x, uint64_t y, uint64_t z, const char* fileNam
}

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;
// Modified to enable looping through tiff dir with user specified steps
for(int64_t dir = startSlice+(w*batchSize*sliceStep); dir < startSlice+((w+1)*batchSize*sliceStep); dir = dir+sliceStep){
// Modified, (z-1)*sliceStep+startSlice is the last slice to read
if(dir>=z*sliceStep+startSlice || err) break;

uint8_t counter = 0;
while(!TIFFSetDirectory(tif, (uint64_t)dir) && counter<3){
Expand Down Expand Up @@ -148,7 +151,7 @@ uint8_t readTiffParallel(uint64_t x, uint64_t y, uint64_t z, const char* fileNam
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)];
((uint8_t*)tiff)[((j*y)+(k+(i*stripSize)))+((dir-startSlice)/sliceStep*(x*y))] = ((uint8_t*)buffer)[j+(k*x)];
}
}
break;
Expand All @@ -157,7 +160,7 @@ uint8_t readTiffParallel(uint64_t x, uint64_t y, uint64_t z, const char* fileNam
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)];
((uint16_t*)tiff)[((j*y)+(k+(i*stripSize)))+((dir-startSlice)/sliceStep*(x*y))] = ((uint16_t*)buffer)[j+(k*x)];
}
}
break;
Expand All @@ -166,7 +169,7 @@ uint8_t readTiffParallel(uint64_t x, uint64_t y, uint64_t z, const char* fileNam
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)];
((float*)tiff)[((j*y)+(k+(i*stripSize)))+((dir-startSlice)/sliceStep*(x*y))] = ((float*)buffer)[j+(k*x)];
}
}
break;
Expand All @@ -175,7 +178,7 @@ uint8_t readTiffParallel(uint64_t x, uint64_t y, uint64_t z, const char* fileNam
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)];
((double*)tiff)[((j*y)+(k+(i*stripSize)))+((dir-startSlice)/sliceStep*(x*y))] = ((double*)buffer)[j+(k*x)];
}
}
break;
Expand All @@ -185,12 +188,12 @@ uint8_t readTiffParallel(uint64_t x, uint64_t y, uint64_t z, const char* fileNam
free(buffer);
TIFFClose(tif);
}
if(err){
if(errBak) return readTiffParallelBak(x, y, z, fileName, tiff, bits, startSlice, flipXY);
else {
printf(errString);
}
}
//if(err){
//if(errBak) return readTiffParallelBak(x, y, z, fileName, tiff, bits, startSlice, flipXY);
//else {
//printf(errString);
//}
//}
return err;
}

Expand Down Expand Up @@ -565,15 +568,15 @@ uint8_t readTiffParallelImageJ(uint64_t x, uint64_t y, uint64_t z, const char* f
return err;
}


// Modified for accepting zRange in the format of both [start end] and [start step end]
// tiff pointer guaranteed to be NULL or the correct size array for the tiff file
void* readTiffParallelWrapperHelper(const char* fileName, void* tiff, uint8_t flipXY, const std::vector<uint64_t> &zRange = {})
{
TIFFSetWarningHandler(DummyHandler);
TIFF* tif = TIFFOpen(fileName, "r");
if(!tif) return NULL;

uint64_t x = 1,y = 1,z = 1,bits = 1, startSlice = 0;
uint64_t x = 1,y = 1,z = 1,bits = 1, startSlice = 0, sliceStep = 1;
TIFFGetField(tif, TIFFTAG_IMAGEWIDTH, &x);
TIFFGetField(tif, TIFFTAG_IMAGELENGTH, &y);
z = getImageSizeZ(fileName);
Expand All @@ -597,6 +600,11 @@ void* readTiffParallelWrapperHelper(const char* fileName, void* tiff, uint8_t fl
startSlice = zRange[0];
z = zRange[1];
}
else if(zRange.size() == 3){
startSlice = zRange[0];
sliceStep = zRange[1];
z = (zRange[2]-zRange[0])/sliceStep+1;
}
else{
startSlice = zRange[0];
z = zRange[0]+1;
Expand Down Expand Up @@ -657,22 +665,22 @@ void* readTiffParallelWrapperHelper(const char* fileName, void* tiff, uint8_t fl
else{
if(bits == 8){
if(!tiff) tiff = (uint8_t*)malloc(x*y*z*sizeof(uint8_t));
readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, stripSize, flipXY);
readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, sliceStep, stripSize, flipXY);
return (void*)tiff;
}
else if(bits == 16){
if(!tiff) tiff = (uint16_t*)malloc(x*y*z*sizeof(uint16_t));
readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, stripSize, flipXY);
readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, sliceStep, stripSize, flipXY);
return (void*)tiff;
}
else if(bits == 32){
if(!tiff) tiff = (float*)malloc(x*y*z*sizeof(float));
readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, stripSize, flipXY);
readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, sliceStep, stripSize, flipXY);
return (void*)tiff;
}
else if(bits == 64){
if(!tiff) tiff = (double*)malloc(x*y*z*sizeof(double));
readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, stripSize, flipXY);
readTiffParallel(x,y,z,fileName, (void*)tiff, bits, startSlice, sliceStep, stripSize, flipXY);
return (void*)tiff;
}
else{
Expand Down
2 changes: 1 addition & 1 deletion src/parallelreadtiff.h
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Expand Up @@ -4,7 +4,7 @@
#include <cstdint>
#include <vector>

uint8_t readTiffParallel(uint64_t x, uint64_t y, uint64_t z, const char* fileName, void* tiff, uint64_t bits, uint64_t startSlice, uint64_t stripSize, uint8_t flipXY);
uint8_t readTiffParallel(uint64_t x, uint64_t y, uint64_t z, const char* fileName, void* tiff, uint64_t bits, uint64_t startSlice, uint64_t sliceStep, uint64_t stripSize, uint8_t flipXY);

uint8_t readTiffParallel2D(uint64_t x, uint64_t y, uint64_t z, const char* fileName, void* tiff, uint64_t bits, uint64_t startSlice, uint64_t stripSize, uint8_t flipXY);

Expand Down