Reading images into vec<Mat> 16bit error - c++

Question

I'm trying to read a 3D image (stored as binary file) into a vector of Mat (so that I could read slice by slice) but always giving me segmentation error when trying to run create_mat. I'm struggling to find what went wrong. Is this the best way to read the data in the first place ?
#include <cstdint>
#include <string>
#include <opencv2/core/core.hpp>
#include <opencv2/highgui/highgui.hpp>
#include <opencv2/imgproc/imgproc.hpp>
#include <iostream>
using namespace cv;
using namespace std;
void read_tiff(string filename,unsigned long length,uint16_t* buffer)
{
//Reads a binary file containing little endean array of uint16_t into a single array pointed by buffer
FILE *ptr_file;
ptr_file = fopen(filename.c_str(),"rb");
rewind(ptr_file);
uint16_t temp;
unsigned int k;
for (k=0;k<length;k++)
{
fread(&temp,2,1,ptr_file);
buffer[k] = temp;
}
fclose(ptr_file);
return;
}
void create_mat(vector<Mat> dst,const int width,const int height,const int stacks,uint16_t* src)
{
int i,j,k;
int counter = 0;
for (i=0;i<stacks;i++)
{
for (j=0;j<height;j++)
{
for (k=0;k<width;k++)
{
(dst[i]).at<ushort>(j,k)= src[counter];
cout<<src[counter]<<endl;
// cout<<dst[i].at<ushort>(j,k)<<endl;
counter++;
}
}
}
}
int main()
{
string dir;
dir = "/somedir.raw";
cout<<dir<<std::endl;
unsigned long length = 1365ul*1531ul*1265ul;
uint16_t test[length];
read_tiff(dir,length,test);
int size[3] = {1265,1365,1531};
vector<Mat> img(size[0],Mat(size[1],size[2],CV_16UC1));
cout <<"image loading done"<<endl;
create_mat(img,size[1],size[2],size[0],test);
imwrite("test.jpg",img[400]);
return 0;
}

Answer 1

Please try this code, which fixes the 2 problems I mentioned in the comments:
Code changes are marked by CHANGED:
#include <cstdint>
#include <string>
#include <opencv2/core/core.hpp>
#include <opencv2/highgui/highgui.hpp>
#include <opencv2/imgproc/imgproc.hpp>
#include <iostream>
using namespace cv;
using namespace std;
void read_tiff(string filename,unsigned long length,uint16_t* buffer)
{
//Reads a binary file containing little endean array of uint16_t into a single array pointed by buffer
FILE *ptr_file;
ptr_file = fopen(filename.c_str(),"rb");
rewind(ptr_file);
uint16_t temp;
unsigned int k;
for (k=0;k<length;k++)
{
fread(&temp,2,1,ptr_file);
buffer[k] = temp;
}
fclose(ptr_file);
return;
}
void create_mat(vector<Mat> dst,const int width,const int height,const int stacks,uint16_t* src)
{
int i,j,k;
int counter = 0;
for (i=0;i<stacks;i++)
{
for (j=0;j<height;j++)
{
for (k=0;k<width;k++)
{
(dst[i]).at<ushort>(j,k)= src[counter];
cout<<src[counter]<<endl;
// cout<<dst[i].at<ushort>(j,k)<<endl;
counter++;
}
}
}
}
int main()
{
string dir;
dir = "/somedir.raw";
cout<<dir<<std::endl;
unsigned long length = 1365ul*1531ul*1265ul;
uint16_t test[length];
read_tiff(dir,length,test);
int size[3] = {1265,1365,1531};
// CHANGED: Instead of allocating Mat memory once and copy-constructing the Mat-header, create a new Mat header + memory for each vector element. Otherwise all the elements will share their pixel data (if you don't call a function that assigns new memory to the Mat)
//vector<Mat> img(size[0],Mat(size[1],size[2],CV_16UC1));
vector<Mat> img(size[0]);
for(int i=0; i<size[0]; ++i)
img[i] = Mat(size[2],size[1],CV_16UC1); // CHANGED: swapped height and width, because Mat constructor uses height-first
cout <<"image loading done"<<endl;
create_mat(img,size[1],size[2],size[0],test);
imwrite("test.jpg",img[400]);
return 0;
}