/**
* Write a ccns_slice object to a repository.
* @param h is the ccn_handle on which to write.
* @param slice is a pointer to a ccns_slice object to be written.
* @param name, if non-NULL, is a pointer to a charbuf which will be filled
* in with the name of the slice that was written.
* @returns 0 on success, -1 otherwise.
*/
int
ccns_write_slice(struct ccn *h,
struct ccns_slice *slice,
struct ccn_charbuf *name) {
struct ccn_charbuf *n = NULL;
int res;
// calculate versioned and segmented name for the slice
n = ccn_charbuf_create();
if (n == NULL)
return(-1);
res = ccns_slice_name(n, slice);
if (res < 0)
goto Cleanup;
res |= ccn_create_version(h, n, CCN_V_NOW, 0, 0);
if (name != NULL) {
ccn_charbuf_reset(name);
res |= ccn_charbuf_append_charbuf(name, n);
}
res |= ccn_name_append_numeric(n, CCN_MARKER_SEQNUM, 0);
if (res < 0)
goto Cleanup;
res = write_slice(h, slice, n);
Cleanup:
ccn_charbuf_destroy(&n);
return (res);
}
/**
* Delete a ccns_slice object from a repository.
* @param h is the ccn_handle on which to write.
* @param name is a pointer to a charbuf naming the slice to be deleted.
* @returns 0 on success, -1 otherwise.
*/
int
ccns_delete_slice(struct ccn *h, struct ccn_charbuf *name) {
struct ccn_charbuf *n = NULL;
int res = 0;
// calculate versioned and segmented name for the slice
n = ccn_charbuf_create_n(32 + name->length);
if (n == NULL)
return(-1);
res |= ccn_charbuf_append_charbuf(n, name);
res |= ccn_create_version(h, n, CCN_V_NOW | CCN_V_REPLACE, 0, 0);
res |= ccn_name_append_numeric(n, CCN_MARKER_SEQNUM, 0);
if (res >= 0)
res = write_slice(h, NULL, n);
ccn_charbuf_destroy(&n);
return (res);
}
int main(int argc, char** argv) {
if (argc < 8) {
std::cout << "usage: watershed <aff_x_dir> <aff_y_dir> <aff_z_dir> <t_l> <t_h> <t_s> <ms>" << std::endl;
return 1;
}
std::string aff_x_dir = argv[1];
std::string aff_y_dir = argv[2];
std::string aff_z_dir = argv[3];
float t_l = boost::lexical_cast<float>(argv[4]);
float t_h = boost::lexical_cast<float>(argv[5]);
float t_s = boost::lexical_cast<float>(argv[6]);
int ms = boost::lexical_cast<float>(argv[7]);
std::cout
<< "Performing affinity graph watershed on volumes "
<< aff_x_dir << ", " << aff_y_dir << ", " << aff_z_dir
<< std::endl;
boost::filesystem::path aff_x_path(aff_x_dir);
boost::filesystem::path aff_y_path(aff_y_dir);
boost::filesystem::path aff_z_path(aff_z_dir);
int size_z = num_files(aff_x_path);
if (size_z != num_files(aff_y_dir) || size_z != num_files(aff_z_dir)) {
std::cerr << "directories contain different number of files" << std::endl;
return 1;
}
if (size_z == 0) {
std::cerr << "directories contain no files" << std::endl;
return 1;
}
std::vector<boost::filesystem::path> aff_x_files = files(aff_x_path);
std::vector<boost::filesystem::path> aff_y_files = files(aff_y_path);
std::vector<boost::filesystem::path> aff_z_files = files(aff_z_path);
aff_x_files.resize(1); // one section only
aff_y_files.resize(1); // one section only
aff_z_files.resize(1); // one section only
size_z = 1;
std::sort(aff_x_files.begin(), aff_x_files.end());
std::sort(aff_y_files.begin(), aff_y_files.end());
std::sort(aff_z_files.begin(), aff_z_files.end());
vigra::ImageImportInfo info(aff_x_files[0].native().c_str());
int size_x = info.width();
int size_y = info.height();
std::cout << "reading affinity graph of size " << size_x << "x" << size_y << "x" << size_z << std::endl;
affinity_graph_ptr<float> aff(
new affinity_graph<float>(
boost::extents[size_x][size_y][size_z][3],
boost::fortran_storage_order()));
for (int z = 0; z < size_z; z++) {
auto slice = (*aff)[ boost::indices[range()][range()][z][range()] ];
read_slice(slice, aff_x_files[z], aff_y_files[z], aff_z_files[z]);
}
std::cout << "performing simple_watershed" << std::endl;
std::vector<std::size_t> counts;
auto result = simple_watershed<uint32_t>(aff, t_l, t_h, counts);
auto segmentation = result.first;
int num_segments = result.second;
std::cout << "found " << num_segments << " segments" << std::endl;
auto rg = get_region_graph<uint32_t,float>(aff, segmentation, num_segments);
std::cout << "performing region merging" << std::endl;
// I guess the last parameter is to discard regions smaller than that
//merge_segments_with_function(result.first, rg, counts,
//dynamic_size_threshold(t_s, ms), 0);
for (int z = 0; z < size_z; z++) {
auto slice = (*segmentation)[ boost::indices[range()][range()][z] ];
std::stringstream filename;
filename << "watershed_" << std::setw(5) << std::setfill('0') << z << "_" << t_l << "_" << t_h << "_" << t_s << "_" << ms << ".tif";
write_slice(slice, filename.str());
}
}
