Geo3d_Scalar_Field* ZNeuronTracer::extractLineSeed(
const Stack *mask, const Stack *dist, int minObjSize)
{
Object_3d_List *objList = Stack_Find_Object_N(
const_cast<Stack*>(mask), NULL, 1, minObjSize, 26);
ZObject3dArray objArray;
objArray.append(objList);
Geo3d_Scalar_Field *field = Make_Geo3d_Scalar_Field(objArray.size());
for (size_t i = 0; i < objArray.size(); ++i) {
ZObject3d *obj = objArray[i];
ZIntPoint pt = obj->getCentralVoxel();
field->points[i][0] = pt.getX();
field->points[i][1] = pt.getY();
field->points[i][2] = pt.getZ();
field->values[i] = sqrt(
C_Stack::value(dist, pt.getX(), pt.getY(), pt.getZ()));
}
return field;
}
int main(int argc, char *argv[])
{
/* Takes '-ver' option and show the version */
if (Show_Version(argc, argv, "0.1") == 1) {
return 0;
}
//For testing
#if 0
Object_3d *obj_test = Make_Object_3d(27, 6);
ndim_type ndim_test = 3;
dim_type dim_test[3] = {3, 3, 3};
FMatrix *detected1_test = FMatrix_Ones(dim_test, ndim_test);
detected1_test->array[0] = 2.0;
detected1_test->array[7] = 2.0;
size_t offset = 0;
for (int k = 0; k < 3; k++) {
for (int j = 0; j < 3; j++) {
for (int i = 0; i < 3; i++) {
obj_test->voxels[offset][0] = i;
obj_test->voxels[offset][1] = j;
obj_test->voxels[offset][2] = k;
offset++;
}
}
}
vector<int> labelArray_test = apply_clustering(obj_test, detected1_test, 3);
return 1;
#endif
#if 1
static const char *Spec[] = {"--result_file <string>",
"--param_file <string> --jsonoutputfile <string>",
"[--test <string>]", "[--golden <string>]", NULL};
ZArgumentProcessor::processArguments(argc, argv, Spec);
cout << argv[0] << " started ..." << endl;
cout << "Parsing parameters ..." << endl;
TbarSaParameter opts;
parse_param(ZArgumentProcessor::getStringArg("--param_file"), &opts);
cout << "TBar width " << opts.tbarWidth << endl;
cout << "cluster_cc " << opts.clusterCC << endl;
cout << "max_cluster_sz " << opts.max_cluster_sz << endl;
cout << "boundary_offset " << opts.offset << endl;
cout << "thds ";
darray_print(&(opts.thds[0]), opts.thds.size());
cout << "min_dist_ctrs " << opts.minDistCtrs << endl;
cout << "save_screenshot " << opts.saveScreenShot << endl;
cout << "Loading result file ..." << endl;
if (opts.saveScreenShot) {
cout << "Screenshot function is not avaible yet" << endl;
//void *vol_all = hdf5read(Get_String_Arg("--result_file"), "volume/data");
//double *vol = hdf5_make_double_array(vol_all, type);
}
FMatrix *detected_all =
hdf5read_prediction(ZArgumentProcessor::getStringArg("--result_file"));
size_t length = Matrix_Size(detected_all->dim, detected_all->ndim);
cout << "Overall length: " << length << endl;
int vold = detected_all->dim[1];
int imh = detected_all->dim[2];
int imw = detected_all->dim[3];
dim_type dims[3];
dims[0] = detected_all->dim[1];
dims[1] = detected_all->dim[2];
dims[2] = detected_all->dim[3];
FMatrix *detected1 = Make_FMatrix(dims, 3);
length = Matrix_Size(detected1->dim, detected1->ndim);
size_t offset_all = 0;
for (size_t offset1 = 0; offset1 < length; offset1++) {
detected1->array[offset1] = detected_all->array[offset_all];
offset_all += detected_all->dim[0];
}
string testDir;
string goldenDir;
if (ZArgumentProcessor::isArgMatched("--golden")) {
goldenDir = ZArgumentProcessor::getStringArg("--golden");
}
if (ZArgumentProcessor::isArgMatched("--test")) {
testDir = ZArgumentProcessor::getStringArg("--test");
}
if (ZArgumentProcessor::isArgMatched("--golden") ||
ZArgumentProcessor::isArgMatched("--test")) {
Stack golden;
golden.kind = FLOAT32;
golden.width = detected1->dim[0];
golden.height = detected1->dim[1];
golden.depth = detected1->dim[2];
golden.array = (uint8*) detected1->array;
golden.text = const_cast<char*>("\0");
if (ZArgumentProcessor::isArgMatched("--golden")) {
Write_Stack(const_cast<char*>((goldenDir + "/detected1.tif").c_str()),
&golden);
}
if (ZArgumentProcessor::isArgMatched("--test")) {
Write_Stack(const_cast<char*>((testDir + "/detected1.tif").c_str()),
&golden);
}
}
//////testing//////////
/*
Stack *stack = Scale_Float_Stack(detected1->array, detected1->dim[0],
detected1->dim[1], detected1->dim[2],
GREY);
Write_Stack("/Users/zhaot/Work/neutube/neurolabi/data/test.tif", stack);
*/
///////////////////
double avg_sz = opts.tbarWidth * opts.tbarWidth * opts.tbarWidth;
double min_sz = avg_sz / 125.0;
double tbar_cube_w = floor(opts.tbarWidth / 2.0);
static const int morpho_w = 3;
Struct_Element *se = Make_Cuboid_Se(morpho_w, morpho_w, morpho_w);
Stack *bb = Make_Stack(GREY, vold, imh, imw);
Stack *bb2 = Make_Stack(GREY, vold, imh, imw);
Stack *bb3 = Make_Stack(GREY, vold, imh, imw);
size_t volume = Stack_Voxel_Number(bb);
for (int ti = 0; ti < opts.thds.size(); ti++) {
double thd = opts.thds[ti];
cout << "thd = " << thd << endl;
for (size_t offset = 0; offset < volume; offset++) {
if (detected1->array[offset] > thd) {
bb->array[offset] = 1;
} else {
bb->array[offset] = 0;
}
}
//Write_Stack(const_cast<char*>("../../../data/test.tif"), bb);
if (ZArgumentProcessor::isArgMatched("--golden")) {
Write_Stack(const_cast<char*>((goldenDir + "/bb.tif").c_str()), bb);
}
if (ZArgumentProcessor::isArgMatched("--test")) {
Write_Stack(const_cast<char*>((testDir + "/bb.tif").c_str()), bb);
}
tic();
Stack_Erode_Fast(bb, bb2, se);
ptoc();
//Write_Stack(const_cast<char*>("../../../data/test2.tif"), bb2);
if (ZArgumentProcessor::isArgMatched("--golden")) {
Write_Stack(const_cast<char*>((goldenDir + "/bb2.tif").c_str()), bb2);
}
if (ZArgumentProcessor::isArgMatched("--test")) {
Write_Stack(const_cast<char*>((testDir + "/bb2.tif").c_str()), bb2);
}
tic();
Stack_Dilate_Fast(bb2, bb3, se);
ptoc();
if (ZArgumentProcessor::isArgMatched("--golden")) {
Write_Stack(const_cast<char*>((goldenDir + "/bb3.tif").c_str()), bb3);
}
if (ZArgumentProcessor::isArgMatched("--test")) {
Write_Stack(const_cast<char*>((testDir + "/bb3.tif").c_str()), bb3);
}
tic();
cout << "Finding objects ..." << endl;
Object_3d_List *objList = Stack_Find_Object_N(bb3, NULL, 1, 0, 6);
ptoc();
if (ZArgumentProcessor::isArgMatched("--golden")) {
Object_3d_List_Export_Csv(const_cast<char*>((goldenDir + "/objlist.csv").c_str()), objList);
}
if (ZArgumentProcessor::isArgMatched("--test")) {
Object_3d_List_Export_Csv(const_cast<char*>((testDir + "/objlist.csv").c_str()), objList);
}
ZObject3dArray objArray;
Object_3d_List *head = objList;
cout << "split objects ..." << endl;
tic();
if (opts.clusterCC) {
while (objList != NULL) {
vector<int> labelArray =
apply_clustering(objList->data, detected1,
opts.max_cluster_sz);
objArray.append(objList->data, labelArray);
//cout << "Object number: " << objArray.size() << endl;
objList = objList->next;
}
Kill_Object_3d_List(head);
} else {
objArray.append(objList);
}
ptoc();
cout << objArray.size() << " objects" << endl;
if (ZArgumentProcessor::isArgMatched("--golden")) {
objArray.exportCsvFile((goldenDir + "/split_objlist.csv").c_str());
}
if (ZArgumentProcessor::isArgMatched("--test")) {
objArray.exportCsvFile((testDir + "/split_objlist.csv").c_str());
}
cout << "Computer centers ..." << endl;
ZObject3d centerArray;
int nselected = 0;
for (size_t i = 0; i < objArray.size(); i++) {
if (objArray[i]->size() >= min_sz) {
nselected++;
//objArray[i]->translate(-1, -1, -1);
ZPoint center = objArray[i]->computeCentroid(detected1);
int x = floor(center.x()) + 1;
int y = floor(center.y()) + 1;
int z = floor(center.z()) + 1;
if (z >= opts.offset &&
z <= (detected1->dim[2] - opts.offset) &&
y >= opts.offset &&
y <= (detected1->dim[1] - opts.offset)) {
centerArray.append(x, y, z);
}
}
}
cout << centerArray.size() << " centers calculated." << endl;
if (ZArgumentProcessor::isArgMatched("--golden")) {
centerArray.exportCsvFile((goldenDir + "/center.csv").c_str());
}
if (ZArgumentProcessor::isArgMatched("--test")) {
centerArray.exportCsvFile((testDir + "/center.csv").c_str());
}
cout << "Merge centers ..." << endl;
vector<size_t> indexArray = centerArray.toIndexArray<size_t>(
detected1->dim[0], detected1->dim[1], detected1->dim[2],
-1, -1, -1);
vector<float> weightArray(indexArray.size());
for (int i = 0; i < indexArray.size(); i++) {
weightArray[i] = detected1->array[indexArray[i]];
}
vector<int> rankArray(indexArray.size());
farray_qsort(&(weightArray[0]), &(rankArray[0]), weightArray.size());
vector<bool> merged(centerArray.size(), false);
int nmerged = 0;
for (int i = centerArray.size() - 1; i >= 0; i--) {
if (!merged[rankArray[i]]) {
for (int j = 0; j < centerArray.size(); j++) {
if (!merged[j] && j != rankArray[i]) {
int dx = centerArray.x(rankArray[i]) - centerArray.x(j);
int dy = centerArray.y(rankArray[i]) - centerArray.y(j);
int dz = centerArray.z(rankArray[i]) - centerArray.z(j);
int d = dx * dx + dy * dy + dz * dz;
if (sqrt(d) < opts.minDistCtrs) {
merged[j] = true;
nmerged++;
}
}
}
}
}
//centerArray.exportSwcFile("/Users/zhaot/Work/neutube/neurolabi/data/test.swc");
cout << nmerged << " merged" << endl;
///test///
if (ZArgumentProcessor::isArgMatched("--golden")) {
ofstream stream((goldenDir + "/merged_center.csv").c_str());
for (size_t i = 0; i < centerArray.size(); i++) {
if (!merged[i]) {
stream << centerArray.x(i) - 1 << "," << centerArray.y(i) - 1 << ","
<< centerArray.z(i) - 1 << endl;
}
}
stream.close();
}
if (ZArgumentProcessor::isArgMatched("--test")) {
ofstream stream((testDir + "/merged_center.csv").c_str());
for (size_t i = 0; i < centerArray.size(); i++) {
if (!merged[i]) {
stream << centerArray.x(i) - 1 << "," << centerArray.y(i) - 1 << ","
<< centerArray.z(i) - 1 << endl;
}
}
stream.close();
}
ofstream stream("/Users/zhaot/Work/neutube/neurolabi/data/test2.swc");
for (size_t i = 0; i < centerArray.size(); i++) {
if (!merged[i]) {
stream << i + 1 << " " << 2 << " "
<< centerArray.x(i) - 1 << " " << centerArray.y(i) - 1 << " "
<< centerArray.z(i) - 1
<< " " << 3.0 << " " << -1 << endl;
}
}
stream.close();
//////////
cout << "Writing results to "
<< ZArgumentProcessor::getStringArg("--jsonoutputfile")
<< "..." << endl;
FILE *jfid = fopen(ZArgumentProcessor::getStringArg(("--jsonoutputfile")),
"w");
fprintf(jfid,"{\n \"data\": [\n");
bool tbarcheck = false;
for (int i = 0; i < centerArray.size(); i++) {
if (!merged[i] /*|| kept[i]*/) {
int mx = centerArray.z(i);
int my = centerArray.y(i);
int mz = centerArray.x(i);
if (tbarcheck) {
fprintf(jfid, ",\n { \n");
} else {
fprintf(jfid, " { \n");
}
fprintf(jfid,"\t \"T-bar\": { \n");
fprintf(jfid,"\t\t\"status\": \"working\", \n");
fprintf(jfid,"\t\t\"confidence\": 1.0, \n");
fprintf(jfid,"\t\t\"body ID\": -1, \n");
fprintf(jfid,"\t\t\"location\": [ \n");
fprintf(jfid,"\t\t %d, \n", mx);
fprintf(jfid,"\t\t %d, \n", detected1->dim[1] - my);
fprintf(jfid,"\t\t %d \n", mz);
fprintf(jfid,"\t\t ] \n");
fprintf(jfid,"\t }, \n");
fprintf(jfid,"\t\"partners\": [ ]\n");
fprintf(jfid," } ");
tbarcheck=true;
}
}
fprintf(jfid,"\n ],\n");
fprintf(jfid," \"metadata\": {\n");
fprintf(jfid,"\t \"username\": \"dummy\",\n");
fprintf(jfid,"\t \"software version\": \"dummy\",\n");
fprintf(jfid,"\t \"description\": \"synapse annotations\",\n");
fprintf(jfid,"\t \"file version\": 1, \n");
fprintf(jfid,"\t \"software version\": \"dummy\",\n");
fprintf(jfid,"\t \"computer\": \"dummy\",\n");
fprintf(jfid,"\t \"date\": \"dummy\",\n");
fprintf(jfid,"\t \"session path\": \"dummy\",\n");
fprintf(jfid,"\t \"software\": \"dummy\"\n");
fprintf(jfid," }\n}");
fclose(jfid);
}
#endif
#ifdef _TEST_
cout << "Testing hdf5 now ... " << endl;
hid_t file_id;
herr_t status;
file_id = H5Fcreate("../../../data/test.h5", H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
status = H5Fclose(file_id);
hid_t dataset_id, dataspace_id;
hsize_t dims[2];
file_id = H5Fcreate("../../../data/test.h5", H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
dims[0] = 4;
dims[1] = 6;
dataspace_id = H5Screate_simple(2, dims, NULL);
dataset_id = H5Dcreate(file_id, "/dset", H5T_STD_I32BE, dataspace_id,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Dclose(dataset_id);
status = H5Sclose(dataspace_id);
status = H5Fclose(file_id);
int i, j, dset_data[4][6];
for (i = 0; i < 4; i++) {
for (j = 0; j < 6; j++) {
dset_data[i][j] = i * 6 + j + 1;
}
}
file_id = H5Fopen("../../../data/test.h5", H5F_ACC_RDWR, H5P_DEFAULT);
dataset_id = H5Dopen(file_id, "/dset", H5P_DEFAULT);
status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
dset_data);
status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
dset_data);
status = H5Dclose(dataset_id);
status = H5Fclose(file_id);
dims[0] = 2;
dims[1] = 3;
int data[6] = {1,2,3,4,5,6};
file_id = H5Fcreate("../../../data/test.h5", H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
status = H5LTmake_dataset(file_id, "/dset", 2, dims, H5T_NATIVE_INT, data);
status = H5Fclose(file_id);
size_t nrow, n_values;
file_id = H5Fopen("../../../data/test.h5", H5F_ACC_RDONLY, H5P_DEFAULT);
status = H5LTread_dataset_int(file_id, "/dset", data);
status = H5LTget_dataset_info(file_id, "/dset", dims, NULL, NULL);
n_values = (size_t) (dims[0] * dims[1]);
nrow = (size_t) dims[1];
cout << n_values << " " << nrow << endl;
for (i = 0; i < n_values / nrow; i++) {
for (j = 0; j < nrow; j++) {
printf(" %d", data[i * nrow + j]);
}
printf("\n");
}
status = H5Fclose(file_id);
hid_t group_id;
file_id = H5Fcreate("../../../data/test.h5", H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
group_id = H5Gcreate(file_id, "/MyGroup", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
status = H5Gclose(group_id);
status = H5Fclose(file_id);
hid_t group1_id, group2_id, group3_id;
file_id = H5Fcreate("../../../data/test.h5", H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
group1_id = H5Gcreate(file_id, "/MyGroup", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
group2_id = H5Gcreate(file_id, "/MyGroup/Group_A", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
group3_id = H5Gcreate(group1_id, "Group_B", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
status = H5Gclose(group1_id);
status = H5Gclose(group2_id);
status = H5Gclose(group3_id);
status = H5Fclose(file_id);
int dset1_data[3][3], dset2_data[2][10];
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) {
dset1_data[i][j] = j + 1;
}
}
for (i = 0; i < 2; i++) {
for (j = 0; j < 10; j++) {
dset2_data[i][j] = j + 1;
}
}
file_id = H5Fopen("../../../data/test.h5", H5F_ACC_RDWR, H5P_DEFAULT);
dims[0] = 3;
dims[1] = 3;
dataspace_id = H5Screate_simple(2, dims, NULL);
dataset_id = H5Dcreate(file_id, "/MyGroup/dset1", H5T_STD_I32BE, dataspace_id,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
dset1_data);
status = H5Sclose(dataspace_id);
status = H5Dclose(dataset_id);
group_id = H5Gopen(file_id, "/MyGroup/Group_A", H5P_DEFAULT);
dims[0] = 2;
dims[1] = 10;
dataspace_id = H5Screate_simple(2, dims, NULL);
dataset_id = H5Dcreate(group_id, "dset2", H5T_STD_I32BE, dataspace_id,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
dset2_data);
status = H5Sclose(dataspace_id);
status = H5Gclose(group_id);
status = H5Fclose(file_id);
cout << "Done!" << endl;
#endif
return 0;
}