volumeFromStack.cpp

This code demonstrates how to create a volume from a series of 2D-images given in user-memory.

This code demonstrates how to create a volume from a series of 2D-images given in user-memory.Many 2D images are in user-memory and represent a volume if stacked together. This code shows how to create ImageView from these 2D images, and then create a Volume from these ImageViews.

#include <iostream>
#include <vector>
 
#include <iolink/view/ImageViewFactory.h>
#include <iolink/view/MultiImageViewFactory.h>
 
using namespace iolink;
 
std::vector<uint8_t> slice_0 = {0, 1, 2,  3,  4,  5,  6,  7,  8,  9,  1, 2,  3,  4,  5,  6,  7,  8,  9,  10,
                                2, 3, 4,  5,  6,  7,  8,  9,  10, 11, 3, 4,  5,  6,  7,  8,  9,  10, 11, 12,
                                4, 5, 6,  7,  8,  9,  10, 11, 12, 13, 5, 6,  7,  8,  9,  10, 11, 12, 13, 14,
                                6, 7, 8,  9,  10, 11, 12, 13, 14, 15, 7, 8,  9,  10, 11, 12, 13, 14, 15, 16,
                                8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18};
std::vector<uint8_t> slice_1 = {1, 2,  3,  4,  5,  6,  7,  8,  9,  10, 2,  3,  4,  5,  6,  7,  8,  9,  10, 11,
                                3, 4,  5,  6,  7,  8,  9,  10, 11, 12, 4,  5,  6,  7,  8,  9,  10, 11, 12, 13,
                                5, 6,  7,  8,  9,  10, 11, 12, 13, 14, 6,  7,  8,  9,  10, 11, 12, 13, 14, 15,
                                7, 8,  9,  10, 11, 12, 13, 14, 15, 16, 8,  9,  10, 11, 12, 13, 14, 15, 16, 17,
                                9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19};
std::vector<uint8_t> slice_2 = {2,  3,  4,  5,  6,  7,  8,  9,  10, 11, 3,  4,  5,  6,  7,  8,  9,  10, 11, 12,
                                4,  5,  6,  7,  8,  9,  10, 11, 12, 13, 5,  6,  7,  8,  9,  10, 11, 12, 13, 14,
                                6,  7,  8,  9,  10, 11, 12, 13, 14, 15, 7,  8,  9,  10, 11, 12, 13, 14, 15, 16,
                                8,  9,  10, 11, 12, 13, 14, 15, 16, 17, 9,  10, 11, 12, 13, 14, 15, 16, 17, 18,
                                10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20};
std::vector<uint8_t> slice_3 = {3,  4,  5,  6,  7,  8,  9,  10, 11, 12, 4,  5,  6,  7,  8,  9,  10, 11, 12, 13,
                                5,  6,  7,  8,  9,  10, 11, 12, 13, 14, 6,  7,  8,  9,  10, 11, 12, 13, 14, 15,
                                7,  8,  9,  10, 11, 12, 13, 14, 15, 16, 8,  9,  10, 11, 12, 13, 14, 15, 16, 17,
                                9,  10, 11, 12, 13, 14, 15, 16, 17, 18, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
                                11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21};
std::vector<uint8_t> slice_4 = {4,  5,  6,  7,  8,  9,  10, 11, 12, 13, 5,  6,  7,  8,  9,  10, 11, 12, 13, 14,
                                6,  7,  8,  9,  10, 11, 12, 13, 14, 15, 7,  8,  9,  10, 11, 12, 13, 14, 15, 16,
                                8,  9,  10, 11, 12, 13, 14, 15, 16, 17, 9,  10, 11, 12, 13, 14, 15, 16, 17, 18,
                                10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
                                12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22};
std::vector<uint8_t> slice_5 = {5,  6,  7,  8,  9,  10, 11, 12, 13, 14, 6,  7,  8,  9,  10, 11, 12, 13, 14, 15,
                                7,  8,  9,  10, 11, 12, 13, 14, 15, 16, 8,  9,  10, 11, 12, 13, 14, 15, 16, 17,
                                9,  10, 11, 12, 13, 14, 15, 16, 17, 18, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
                                11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,
                                13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23};
std::vector<uint8_t> slice_6 = {6,  7,  8,  9,  10, 11, 12, 13, 14, 15, 7,  8,  9,  10, 11, 12, 13, 14, 15, 16,
                                8,  9,  10, 11, 12, 13, 14, 15, 16, 17, 9,  10, 11, 12, 13, 14, 15, 16, 17, 18,
                                10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
                                12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
                                14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24};
std::vector<uint8_t> slice_7 = {7,  8,  9,  10, 11, 12, 13, 14, 15, 16, 8,  9,  10, 11, 12, 13, 14, 15, 16, 17,
                                9,  10, 11, 12, 13, 14, 15, 16, 17, 18, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
                                11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,
                                13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
                                15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25};
std::vector<uint8_t> slice_8 = {8,  9,  10, 11, 12, 13, 14, 15, 16, 17, 9,  10, 11, 12, 13, 14, 15, 16, 17, 18,
                                10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
                                12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
                                14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
                                16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26};
std::vector<uint8_t> slice_9 = {9,  10, 11, 12, 13, 14, 15, 16, 17, 18, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
                                11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,
                                13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
                                15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
                                17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27};
 
// here is a vector where all slices of the volume are stored as pointers to the slice data
std::vector<std::vector<uint8_t>> listSlices = {
  slice_0, slice_1, slice_2, slice_3, slice_4, slice_5, slice_6, slice_7, slice_8, slice_9};
 
// create a ImageView for the slice whose data, shape and datatype are given in parameters.
std::shared_ptr<ImageView>
createSliceFromRawData(const std::vector<uint8_t> sliceData, const VectorXu64& sliceShape, DataType dtype)
{
  RegionXu64 fullRegion = RegionXu64::createFullRegion(sliceShape);
 
  // create an image view using user-memory data for each slice
  std::shared_ptr<ImageView> slice = ImageViewFactory::allocate(sliceShape, dtype);
 
  // write data
  slice->writeRegion(fullRegion, sliceData.data());
 
  // update properties of the slice
  slice->setAlpha(false);
  slice->setAxesInterpretation(AxesInterpretationId::IMAGE);
  slice->setImageInterpretation(ImageInterpretation::GRAYSCALE);
 
  return slice;
}
 
// create the volume from slices
std::shared_ptr<ImageView>
createVolumeFromSlices(std::vector<std::vector<uint8_t>>& slices)
{
  // create a MultiImageView from all ImageViews
  std::shared_ptr<MultiImageView> sliceContainer = MultiImageViewFactory::create();
 
  VectorXu64 shapeSlice{10, 10};
  DataType dtype = DataTypeId::UINT8;
 
  // iterate over all slices
  for (size_t i = 0; i < slices.size(); ++i)
  {
    // create an ImageView from the slice data
    std::shared_ptr<ImageView> slice = createSliceFromRawData(slices[i], shapeSlice, dtype);
 
    // add the slice to the MultiImageView
    sliceContainer->addFrame(slice);
  }
 
  // create the volume by indicating the new dimension as SLICE
  return ImageViewFactory::stack(sliceContainer, ImageDimension::SLICE);
}
 
int
main(int argc, char** argv)
{
  // create the volume using the list of slices in user-memory
  std::shared_ptr<ImageView> volume = createVolumeFromSlices(listSlices);
 
  std::cout << "Image created: " << volume->toString() << std::endl;
 
  return EXIT_SUCCESS;
}