[Olena-patches] r3704: Add binary tools for parsing of .mat files

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-24 Fabien Freling &lt;fabien.freling(a)lrde.epita.fr&gt; Add binary tools for parsing of .mat files. * fabien/igr/mat2mln/mat2raw.cc: Uncompress .mat data. * fabien/igr/mat2mln/raw2mlndata.cc: Convert uncompressed .mat data to Milena dump format. * fabien/igr/seg_fixed.cc: Creation of edges between pixels. --- TODO | 4 + igr/mat2mln/mat2raw.cc | 52 ++++++++++++++++++++ igr/mat2mln/raw2mlndata.cc | 113 +++++++++++++++++++++++++++++++++++++++++++++ igr/seg_fixed.cc | 25 ++++++--- 4 files changed, 184 insertions(+), 10 deletions(-) Index: trunk/milena/sandbox/fabien/igr/seg_fixed.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/seg_fixed.cc (revision 3703) +++ trunk/milena/sandbox/fabien/igr/seg_fixed.cc (revision 3704) @@ -59,6 +59,8 @@ res += std::min(ima_arr(p)[i], ima_arr(n)[i]); res /= std::max(ima_sum(p), ima_sum(n)); + std::cout << "dist = " << res << std::endl; + return res; } @@ -87,15 +89,21 @@ initialize(ima_sum, ima_arr); compute_sum_arrays(ima_sum, ima_arr); + std::cout << "can i has a loop?" << std::endl; mln_piter(image2d<util::array<I> >) p(ima_arr.domain()); - mln_niter(neighb2d) n(c4(), p); for_all(p) + { + std::cout << "for_all(p)" << std::endl; + mln_niter(neighb2d) n(c4(), p); for_all(n) { + std::cout << "for_all(n)" << std::endl; point2d location = get_edge_location(p, n); - if (edges(location) != -1) + std::cout << "location = " << p << " && edge = " << edges(location) << std::endl; + if (edges(location) == -1.f) edges(location) = compute_dist(ima_arr, ima_sum, p, n); } + } return edges; } @@ -112,23 +120,22 @@ int main(int argc, char* argv[]) { - typedef int_u12 I; - if (argc != 2) return usage(argv[0]); - image3d<I> input; - io::dump::save(input, argv[1]); - image2d<util::array<I> > ima_arr; + image3d<int_u12> input; + io::dump::load(input, argv[1]); + image2d<util::array<int_u12> > ima_arr; initialize(ima_arr, slice(input, 0)); for (unsigned int i = 0; i < input.nslices(); ++i) { - image2d<I> tmp_slice = duplicate(slice(input, i)); - mln_piter_(image2d<I>) p(tmp_slice.domain()); + image2d<int_u12> tmp_slice = duplicate(slice(input, i)); + mln_piter_(image2d<int_u12>) p(tmp_slice.domain()); for_all(p) ima_arr(p).append(tmp_slice(p)); } + std::cout << "ho hai _o/" << std::endl; image2d<float> edges = dist_on_edges(ima_arr); return 0; Index: trunk/milena/sandbox/fabien/igr/mat2mln/raw2mlndata.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/mat2mln/raw2mlndata.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/mat2mln/raw2mlndata.cc (revision 3704) @@ -0,0 +1,113 @@ +#include <iostream> +#include <fstream> + +#include <mln/core/image/image3d.hh> +#include <mln/io/dump/save.hh> + +using namespace mln; + + +int main(int argc, char* argv[]) +{ + if (argc != 3) + { + std::cout << "Usage: " << argv[0] << " input.raw output.raw" << std::endl; + return 1; + } + + std::ifstream input(argv[1]); + + unsigned int size = 0; + unsigned int offset = 0; + + // Top level miMATRIX. + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Size: " << size << std::endl; + + // Array flags. + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Flags size: " << size << std::endl; + + // Dimensions array. + offset += size; + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Dimensions size: " << size << std::endl; + + // Array name. + offset += size; + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Name size: " << size << std::endl; + char* name = new char[size + 1]; + input.seekg(offset); + input.read((char*) name, size); + name[size + 1] = '\0'; + std::cout << "Array name: " << name << std::endl; + delete name; + offset += 8 - size % 8; + + std::cout << "----" << std::endl; + // FIXME: Decode data. + + offset = 128; + + // Data miMATRIX. + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Data size: " << size << std::endl; + + // Array flags. + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Flags size: " << size << std::endl; + + // Dimensions array. + offset += size; + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Dimensions size: " << size << std::endl; + std::cout << "Number of dimensions: " << size / 4 << std::endl; + int ncols = 0; + int nrows = 0; + int nslis = 0; + input.seekg(offset); + input.read((char*) &ncols, sizeof (unsigned int)); + offset += sizeof (unsigned int); + input.seekg(offset); + input.read((char*) &nrows, sizeof (unsigned int)); + offset += sizeof (unsigned int); + input.seekg(offset); + input.read((char*) &nslis, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "ncols: " << ncols << "; nrows: " << nrows << "; nslis: " << nslis << std::endl; + + // Data buffer. + typedef double V; + int data_size = ncols * nrows * nslis; + V* data_buffer = new V[data_size]; + input.seekg(offset); + input.read((char*) data_buffer, data_size); + + image3d<V> ima(nslis, nrows, ncols); + memcpy(ima.buffer(), data_buffer, data_size); + io::dump::save(ima, argv[2]); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/mat2mln/mat2raw.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/mat2mln/mat2raw.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/mat2mln/mat2raw.cc (revision 3704) @@ -0,0 +1,52 @@ +#include <iostream> +#include <fstream> + +#include <zlib.h> + +int main(int argc, char* argv[]) +{ + if (argc != 3) + { + std::cout << "Usage: " << argv[0] << " input.mat output.raw" << std::endl; + return 1; + } + + std::ifstream input(argv[1]); + + // Fetch data. + unsigned int size; + input.seekg(132); + input.read((char*) &size, sizeof(unsigned int)); + std::cout << "Size: " << size << std::endl; + unsigned char* data_buffer = new unsigned char[size]; + input.read((char*) data_buffer, size); + input.close(); + + // Decompress. + unsigned long dest_size = 2 * size; + unsigned char* dest_buffer = new unsigned char[dest_size]; + int dezip_result = uncompress(dest_buffer, &dest_size, data_buffer, size); + + switch (dezip_result) + { + case Z_OK: + std::cout << "Z_OK" << std::endl; + std::cout << "Dest size: " << dest_size << std::endl; + break; + case Z_MEM_ERROR: + std::cout << "Z_MEM_ERROR" << std::endl; + break; + case Z_BUF_ERROR: + std::cout << "Z_BUF_ERROR" << std::endl; + break; + case Z_DATA_ERROR: + std::cout << "Z_DATA_ERROR" << std::endl; + break; + } + + // Write buffer to disk. + std::ofstream save_file(argv[2]); + save_file.write((char*) dest_buffer, dest_size); + + return 0; +} Index: trunk/milena/sandbox/fabien/TODO =================================================================== --- trunk/milena/sandbox/fabien/TODO (revision 3703) +++ trunk/milena/sandbox/fabien/TODO (revision 3704) @@ -49,7 +49,7 @@ [X] Fix spatial smooth [X] Crop volume 52 [X] Plot all labels (3, 4 labels for tumeur) -[ ] Prepare data for IGR +[X] Prepare data for IGR [X] crop->norm->tmax [X] crop->norm->space_smooth->tmax @@ -64,3 +64,5 @@ [X] fausses couleurs watershed [X] images moyennes +[ ] Watershed between pixels +[ ] Mat2Mln