int main(int argc, char* argv[])
{
char neuron_name[100];
if (argc == 1) {
strcpy(neuron_name, "fly_neuron");
} else {
strcpy(neuron_name, argv[1]);
}
char file_path[100];
sprintf(file_path, "../data/%s/soma.tif", neuron_name);
Stack *stack = Read_Stack(file_path);
Stack_Threshold(stack, 1);
Stack_Binarize(stack);
sprintf(file_path, "../data/%s/mask.tif", neuron_name);
Stack *stack2 = Read_Stack(file_path);
Stack_Xor(stack, stack2, stack2);
sprintf(file_path, "../data/%s/bundle.tif", neuron_name);
Write_Stack(file_path, stack2);
printf("%s created.\n", file_path);
/*
Struct_Element *se = Make_Cuboid_Se(3, 3, 3);
Stack *stack3 = Stack_Dilate(stack, NULL, se);
Stack_And(stack3, stack2, stack2);
sprintf(file_path, "../data/%s/objseed.tif", neuron_name);
Write_Stack(file_path, stack2);
*/
return 0;
}
int main(int argc, char* argv[])
{
char neuron_name[100];
if (argc == 1) {
strcpy(neuron_name, "fly_neuron");
} else {
strcpy(neuron_name, argv[1]);
}
char file_path[100];
sprintf(file_path, "../data/%s/mask.tif", neuron_name);
Stack *mask = Read_Stack(file_path);
sprintf(file_path, "../data/%s/blobmask.tif", neuron_name);
Stack *blobmask = Read_Stack(file_path);
int voxel_number = Stack_Voxel_Number(mask);
int i;
for (i = 0; i < voxel_number; i++) {
if (blobmask->array[i] > 0) {
mask->array[i] = 3;
}
}
sprintf(file_path, "../data/%s/soma.tif", neuron_name);
Write_Stack(file_path, mask);
Kill_Stack(mask);
Kill_Stack(blobmask);
return 0;
}
int main(int argc, char* argv[]) {
char neuron_name[100];
if (argc == 1) {
strcpy(neuron_name, "fly_neuron");
} else {
strcpy(neuron_name, argv[1]);
}
char file_path[100];
sprintf(file_path, "../data/%s/soma.tif", neuron_name);
Stack *stack = Read_Stack(file_path);
int i;
int n = Stack_Voxel_Number(stack);
for (i = 0; i < n; i++) {
stack->array[i] = (stack->array[i] == 2);
}
sprintf(file_path, "../data/%s/arbor.tif", neuron_name);
Write_Stack(file_path, stack);
Kill_Stack(stack);
return 0;
}
int main(int argc, char* argv[])
{
char neuron_name[100];
if (argc == 1) {
strcpy(neuron_name, "fly_neuron");
} else {
strcpy(neuron_name, argv[1]);
}
char file_path[100];
sprintf(file_path, "../data/%s/blobmask.tif", neuron_name);
Stack *stack1 = Read_Stack(file_path);
Stack *stack2 = Copy_Stack(stack1);
int i;
for (i = 0; i < nvoxel; i++) {
stack2->array[i] = 3;
}
sprintf(file_path, "../data/%s/soma.tif", neuron_name);
Write_Stack(file_path, stack2);
Kill_Stack(stack1);
Kill_Stack(stack2);
return 0;
}
/*
* bwdist - build a distance map for a binary stack
*
* bwdist [-b<int>] infile -o outfile
*
* -i: inverse the image
* -b: byte number for output file (1 (default) or 2)
* -sq: build square distance map
*/
int main(int argc, char *argv[])
{
static char *Spec[] = {"<image:string> -o <string>",
"[-b<int> | -sq] [-i] [--plane]",
NULL};
Process_Arguments(argc, argv, Spec, 1);
char *image_file = Get_String_Arg("image");
Stack *stack = Read_Stack(image_file);
if (Is_Arg_Matched("-i")) {
Stack_Not(stack, stack);
}
Stack *distmap = NULL;
if (!Is_Arg_Matched("-sq")) {
distmap = Stack_Bwdist_L(stack, NULL, NULL);
Kill_Stack(stack);
int kind = GREY;
if (Is_Arg_Matched("-b")) {
kind = Get_Int_Arg("-b");
}
stack = Scale_Float_Stack((float *) distmap->array, distmap->width,
distmap->height, distmap->depth, kind);
Kill_Stack(distmap);
distmap = stack;
} else {
if (Is_Arg_Matched("--plane")) {
distmap = Stack_Bwdist_L_U16P(stack, NULL, 0);
Translate_Stack(distmap, GREY, 1);
} else {
distmap = Stack_Bwdist_L_U16(stack, NULL, 0);
}
Kill_Stack(stack);
}
char *out_file = Get_String_Arg("-o");
Write_Stack(out_file, distmap);
Kill_Stack(distmap);
return 1;
}
int main(int argc, char* argv[]) {
Stack *stack = Read_Stack("../data/lobster_neuron_single.tif");
Stack_Not(stack, stack);
Stack *dist = Stack_Bwdist(stack);
Stack *seeds = Stack_Local_Max(dist, NULL, STACK_LOCMAX_ALTER1);
Write_Stack("../data/lobster_neuron_seed.tif", seeds);
Voxel_List *list = Stack_To_Voxel_List(seeds);
Pixel_Array *pa = Voxel_List_Sampling(dist, list);
Pixel_Array_Write("../data/lobster_neuron_seeds.pa", pa);
return 0;
}
/**
* Find the background of a tif stack.
* Output : integer
* Input : stack file or bundle file.
*/
void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[])
{
if (nrhs != 1)
mexErrMsgTxt("The function takes 1 argument.");
if ( !mxIsChar(prhs[0]) )
mexErrMsgTxt("The argument must be a string");
char *filePath = mxArrayToString(prhs[0]);
Stack *stack = NULL;
if( strlen(filePath)>4 ) {
if( Is_Tiff(filePath) ) /* Read file */
stack = Read_Stack(filePath);
else if ( Is_Fbdf(filePath) ) { /* Read directory */
File_Bundle fb;
initfb(&fb);
if( Load_Fbdf(filePath,&fb) )
stack = Read_Stack_Planes(&fb);
freefb(&fb);
} else
mexErrMsgTxt("Unrecongnized file format.");
} else {
mexErrMsgTxt("Unrecongnized file format.");
}
if( stack==NULL )
mexErrMsgTxt("Unable to load the stack.");
if( stack->kind==GREY || stack->kind==GREY16 ) {
int *hist = Stack_Hist(stack);
int hist_size = hist[0] + 2;
plhs[0] = mxCreateNumericMatrix(hist_size,1,mxINT32_CLASS,mxREAL);
int i;
int32_t *hist_pointer = (int32_t *) mxGetPr(plhs[0]);
for(i = 0; i < hist_size; i++)
hist_pointer[i] = hist[i];
free(hist);
Kill_Stack(stack);
} else {
Kill_Stack(stack);
mexErrMsgTxt("Unsupported image format.");
}
}
Stack *load( char *path )
{ char *ext = strrchr( path, '.' );
Stack *s;
if( strcmp(ext,".tif")==0 || strcmp(ext,".tiff")==0 )
{ s = Read_Stack(path);
} else if( strcmp(ext,".seq")==0 )
{ SeqReader *f = Seq_Open(path);
if( !f )
{ fprintf(stderr, "Couldn't open file %s", path );
exit(1);
}
s = Seq_Read_Stack(f);
Seq_Close(f);
}
adjust_scan_bias(s);
return s;
}
int main(int argc, char *argv[])
{
static char *Spec[] = {"<input:string> -o <string> [--dim <string>]", NULL};
Process_Arguments(argc, argv, Spec, 1);
if (Is_Arg_Matched("--dim")) {
if (strcmp(Get_String_Arg("--dim"), "x") == 0 ||
strcmp(Get_String_Arg("--dim"), "X") == 0) {
Stack *stack = Read_Stack(Get_String_Arg("input"));
Image *image = Proj_Stack_Xmax(stack);
Write_Image(Get_String_Arg("-o"), image);
}
} else {
Mc_Stack *stack = Read_Mc_Stack(Get_String_Arg("input"), -1);
Mc_Stack *proj = Mc_Stack_Mip(stack);
Write_Mc_Stack(Get_String_Arg("-o"), proj, NULL);
}
return 0;
}
int main(int argc, char* argv[])
{
char neuron_name[100];
if (argc == 1) {
strcpy(neuron_name, "fly_neuron");
} else {
strcpy(neuron_name, argv[1]);
}
char file_path[100];
sprintf(file_path, "../data/%s/mask.tif", neuron_name);
Stack *mask = Read_Stack(file_path);
sprintf(file_path, "../data/%s/seeds.pa", neuron_name);
Pixel_Array *pa = Pixel_Array_Read(file_path);
double *pa_array = (double *) pa->array;
sprintf(file_path, "../data/%s/seed_offset.ar", neuron_name);
int seed_number = pa->size;
int *seed_offset = (int *) malloc(sizeof(int) * seed_number);
iarray_read(file_path, seed_offset, &seed_number);
int max_idx;
double max_dist = darray_max(pa_array, pa->size, &max_idx);
max_idx = seed_offset[max_idx];
Stack_Label_Object_Dist_N(mask, NULL, max_idx, 1, 2, max_dist * 2.0, 26);
Stack_Threshold_Binarize(mask, 1);
sprintf(file_path, "../data/%s/blobmask.tif", neuron_name);
Write_Stack(file_path, mask);
free(seed_offset);
Kill_Stack(mask);
return 0;
}
int main(int argc, char *argv[])
{
static char *Spec[] = {"<image:string> -s <int> -o <string>",
"[-n <int>]",
NULL};
Process_Arguments(argc, argv, Spec, 1);
Stack *stack = Read_Stack(Get_String_Arg("image"));
int n_nbr = 26;
if (Is_Arg_Matched("-n")) {
n_nbr = Get_Int_Arg("-n");
}
Stack_Label_Large_Objects_N(stack, NULL, 1, 2, Get_Int_Arg("-s") + 1, n_nbr);
Stack_Threshold_Binarize(stack, 2);
Write_Stack(Get_String_Arg("-o"), stack);
return 0;
}
int main(int argc, char* argv[])
{
#if 0
Mc_Stack *mc_stack = Read_Mc_Stack("../data/benchmark/L3_12bit.lsm", -1);
Stack *stack = Mc_Stack_To_Stack(mc_stack, COLOR, NULL);
Write_Stack_U("../data/test.lsm", stack, "../data/benchmark/L3_12bit.lsm");
#endif
#if 0
//Print_Lsm_Info("/Users/zhaot/Data/stitching_12bit/70208_2BcPhR_R1_GR1_B1_L001.lsm");
Mc_Stack *stack = Read_Mc_Stack("../data/benchmark/L3_12bit.lsm", -1);
Print_Mc_Stack_Info(stack);
Mc_Stack_Grey16_To_8(stack, 1);
Write_Mc_Stack("../data/test.lsm", stack, "../data/benchmark/L3_12bit.lsm");
#endif
#if 0
Read_Stack("/Users/zhaot/Data/slice15overlay/L05.tif");
#endif
#if 0
/*
char *filePath = "test";
if( strlen(filePath)>4 )
if( strcmp(filePath+strlen(filePath)-4,".tif")==0 ||
strcmp(filePath+strlen(filePath)-4,".TIF")==0 )
printf("%d\n", 1);
printf("%d\n", 0);
*/
Is_Tiff("test");
//Write_Stack("/Users/zhaot/Work/neurolabi/data/test.tif", Read_Stack("/Users/zhaot/Data/slice15overlay/L03.tif"));
Write_Stack("../data/test.tif", Read_Stack("../data/L05.tif"));
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron.tif");
Write_Stack("../data/test2.tif", stack);
#endif
#if 0
int big_endian;
Tiff_Reader *tif = Open_Tiff_Reader("/Users/zhaot/Data/Stacks for stitching/Set 1 65C07/GL_100708_R1_GR1_B1_L013.lsm", &big_endian, 1);
Tiff_Writer *tif2 = Open_Tiff_Writer("../data/test.tif", 0);
Tiff_IFD *ifd = NULL;
int depth = 0;
while ((ifd = Read_Tiff_IFD(tif)) != NULL) {
if (Convert_LSM_2_RGB(ifd, 0, 0) != NULL) {
Write_Tiff_IFD(tif2, ifd);
depth++;
}
Free_Tiff_IFD(ifd);
}
printf("%d\n", depth);
//Kill_Tiff_IFD(ifd);
Kill_Tiff_Reader(tif);
Close_Tiff_Writer(tif2);
Stack *stack = Read_Stack("../data/test.tif");
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Tiff_Reader *reader;
reader = Open_Tiff_Reader("../data/test.lsm",NULL,1);
Tiff_IFD *ifd = Read_Tiff_IFD(reader);
Print_Tiff_IFD(ifd, stdout);
Kill_Tiff_Reader(reader);
#endif
#if 0
Stack *stack = Read_Lsm_Stack("/Users/zhaot/Data/stitch/Set 3 17F12/GL_100208_R1_GR1_B1_L07.lsm", -1);
//Stack *stack = Read_Lsm_Stack("/Users/zhaot/Data/nathan/2p internal[497-545,565-649nm] 40x 2x12us 900nm 5pct cleared 1.lsm", 0);
Tiff_IFD *ifd;
{ Tiff_Reader *reader;
reader = Open_Tiff_Reader("/Users/zhaot/Data/stitch/Set 3 17F12/GL_100208_R1_GR1_B1_L08.lsm",NULL,1);
while (lsm_thumbnail_flag(ifd = Read_Tiff_IFD(reader)) != 0) {
//Advance_Tiff_Reader(reader);
if (End_Of_Tiff(reader)) {
ifd = NULL;
TZ_ERROR(ERROR_IO_READ);
break;
}
}
}
//Write_Stack("../data/test.tif", stack);
Print_Tiff_IFD(ifd, stdout);
if (stack != NULL) {
Write_Lsm_Stack("../data/test.lsm", stack, ifd);
}
stack = Read_Lsm_Stack("../data/test.lsm", -1);
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Mc_Stack *mc_stack = Read_Mc_Stack("../data/test.tif", 1);
Print_Mc_Stack_Info(mc_stack);
Write_Mc_Stack("../data/test2.tif", mc_stack, NULL);
Free_Mc_Stack(mc_stack);
mc_stack = Read_Mc_Stack("../data/test2.tif", -1);
Print_Mc_Stack_Info(mc_stack);
printf("%d\n", Mc_Stack_Usage());
#endif
#if 0
Stack *stack = Read_Lsm_Stack("../data/test.lsm", -1);
Print_Stack_Info(stack);
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Fix_Lsm_File("../data/test/result1.lsm");
Print_Lsm_Info("../data/test/result1.lsm");
#endif
#if 0
Stack *stack = Make_Stack(1, 5, 5, 5);
int nvoxel = Stack_Voxel_Number(stack);
int i;
for (i = 0; i < nvoxel; i++) {
stack->array[i] = i;
}
Write_Stack("../data/test.tif", stack);
stack = Read_Stack("../data/test.tif");
Write_Stack("../data/test2.tif", stack);
#endif
#if 0
Stack *stack = Read_Stack(fullpath("../data/fly_neuron_n11/", "mask2.tif",
NULL));
Print_Stack_Info(stack);
#endif
#if 0
//Print_Lsm_Info("/Users/zhaot/Data/stitch/Set 3 17F12/GL_100208_R1_GR1_B1_L07.lsm");
//FILE *fp = fopen("/Users/zhaot/Data/stitch/set1/GL_100708_R1_GR1_B1_L015.lsm", "r");
FILE *fp = fopen("../data/test.lsm", "r");
char endian[3];
endian[2] = '\0';
fread(endian, 1, 2, fp);
printf("Endian: %s\n", endian);
uint16_t magic;
fread(&magic, 2, 1, fp);
printf("Magic number: %u\n", magic);
uint32_t ifd_offset;
fread(&ifd_offset, 4, 1, fp);
printf("1st IFD offset: %u\n", ifd_offset);
fseek(fp, ifd_offset, SEEK_SET);
uint16_t nifd;
fread(&nifd, 2, 1, fp);
printf("Number of IFD: %u\n", nifd);
uint16_t ifd_label;
fread(&ifd_label, 2, 1, fp);
uint16_t i;
for (i = 1; i < nifd; i++) {
if (ifd_label == TIF_CZ_LSMINFO) {
break;
}
fseek(fp, 10, SEEK_CUR);
fread(&ifd_label, 2, 1, fp);
}
printf("IFD label: %u\n", ifd_label);
uint16_t ifd_type;
fread(&ifd_type, 2, 1, fp);
printf("IFD type: %u\n", ifd_type);
uint32_t ifd_length;
fread(&ifd_length, 4, 1, fp);
printf("IFD length: %u\n", ifd_length);
fread(&ifd_offset, 4, 1, fp);
printf("Lsm info offset: %u\n", ifd_offset);
/*
fseek(fp, ifd_offset + CZ_LSMINFO_DIMZ_OFFSET, SEEK_SET);
int32_t dimz = 80;
fwrite(&dimz, 4, 1, fp);
printf("Number of slices: %d\n", dimz);
*/
int offset = 88;
fseek(fp, ifd_offset, SEEK_SET);
/*
uint32_t value = 0;
fwrite(&value, 4, 1, fp);
fseek(fp, ifd_offset + offset, SEEK_SET);
*/
/*
Fprint_File_Binary(fp, 24, stdout);
fclose(fp);
return 1;
*/
Cz_Lsminfo lsminfo;
fread(&lsminfo, sizeof(Cz_Lsminfo), 1, fp);
printf("%lu\n", sizeof(Cz_Lsminfo));
if (lsminfo.u32MagicNumber == 67127628) {
printf("Version 1.5, 1.6 and 2.0\n");
} else if (lsminfo.u32MagicNumber == 50350412) {
printf("Version 1.3\n");
} else {
printf("Unknown version\n");
return 1;
}
printf("Structure size: %d\n", lsminfo.s32StructureSize);
printf("Stack size: %d x %d x %d\n", lsminfo.s32DimensionX,
lsminfo.s32DimensionY, lsminfo.s32DimensionZ);
printf("Number of channels: %d\n", lsminfo.s32DimensionChannels);
switch (lsminfo.s32DataType) {
case 1:
printf("8-bit unsigned integer.\n");
break;
case 2:
printf("12-bit unsigned integer.\n");
break;
case 5:
printf("32-bit float.\n");
break;
case 0:
printf("Different channels have different types.\n");
break;
}
printf("Thumbnail size: %d x %d\n", lsminfo.s32ThumbnailX,
lsminfo.s32ThumbnailY);
printf("Voxel size: %g x %g x %g um\n", lsminfo.f64VoxelSizeX * 1000000,
lsminfo.f64VoxelSizeY * 1000000, lsminfo.f64VoxelSizeZ * 1000000);
printf("Scan type: ");
switch (lsminfo.u16ScanType) {
case 0:
printf("normal x-y-z-scan\n");
break;
case 1:
printf("Z-Scan\n");
break;
case 2:
printf("Line Scan\n");
break;
case 3:
printf("Time series x-y\n");
break;
case 4:
printf("Time series x-z\n");
break;
case 5:
printf("Time series - Mean of ROIS\n");
break;
}
if (lsminfo.u32OffsetVectorOverlay == 0) {
printf("There is no vector overlay\n");
} else {
printf("Vector overlay found\n");
}
if (lsminfo.u32OffsetInputLut == 0) {
printf("There is no input LUT\n");
} else {
printf("Input LUT found\n");
}
if (lsminfo.u32OffsetOutputLut == 0) {
printf("There is no color palette\n");
} else {
printf("Color palette found\n");
}
if (lsminfo.u32OffsetChannelColors == 0) {
printf("There is no channel color or channel name\n");
} else {
printf("Channel colors and channel names fournd\n");
}
if (lsminfo.f64TimeInterval == 0) {
printf("There is no time interval\n");
} else {
printf("Time interval: %lg sec\n", lsminfo.f64TimeInterval);
}
if (lsminfo.u32OffsetScanInformation == 0) {
printf("There is no information about devide settings\n");
} else {
printf("Scan information found. Offset: %u\n",
lsminfo.u32OffsetScanInformation);
/*
Lsm_Scan_Info *info =
(Lsm_Scan_Info*) (data + lsminfo.u32OffsetScanInformation + 20);
printf("Information type: %u\n", info->u32Entry);
printf("Data type: %u\n", info->u32Type);
printf("Data size: %u\n", info->u32Size);
*/
/*
uint8_t *byte = (uint8_t*) (data + lsminfo.u32OffsetScanInformation);
printf("%u\n", byte[8]);
*/
}
if (lsminfo.u32OffsetKsData == 0) {
printf("There is no Zeiss Vision KS-3d data\n");
} else {
printf("Zeiss Vision KS-3d data found. Offset: %u\n",
lsminfo.u32OffsetKsData);
}
if (lsminfo.u32OffsetRoi == 0) {
printf("There is no ROI\n");
} else {
printf("ROI found\n");
}
if (lsminfo.u32OffsetNextRecording == 0) {
printf("There is no second image\n");
} else {
printf("Second image found\n");
}
fclose(fp);
#endif
#if 0
FILE *fp = fopen("/Users/zhaot/Data/stitch/set1/GL_100708_R1_GR1_B1_L014.lsm", "r+");
char endian[3];
endian[2] = '\0';
fread(endian, 1, 2, fp);
printf("Endian: %s\n", endian);
fpos_t pos;
fgetpos(fp, &pos);
printf("%d\n", pos);
fseek(fp, 0, SEEK_SET);
uint32_t x = 254;
printf("%lu bytes written\n", fwrite(&x, sizeof(uint32_t), 1, fp));
fgetpos(fp, &pos);
printf("%d\n", pos);
Fprint_File_Binary(fp, 8, stdout);
fclose(fp);
#endif
#if 0
Stack *stack = Read_Lsm_Stack("../data/GL_100208_R1_GR1_B1_L07.lsm", -1);
Write_Stack_U("../data/test.lsm", stack,
"../data/GL_100208_R1_GR1_B1_L07.lsm");
#endif
#if 0
//Stack *stack = Read_Lsm_Stack("/Users/zhaot/Data/neurolineage/lsm/Twin-Spot_Gal4-GH146_nc_11-2.lsm", 0);
Stack *stack = Read_Stack_U("../data/test2.tif");
Write_Stack_U("../data/test.tif", stack, NULL);
#endif
#if 0
Stack *stack = Read_Stack("../data/mouse_single_org/traced.tif");
Write_Stack("../data/test.tif", stack);
#endif
#if 0 /* test writing large stack */
Mc_Stack *stack = Make_Mc_Stack(GREY, 1024, 1024, 1024, 3);
size_t n = (size_t) 1024 * 1024 * 1024 * 3;
size_t i;
for (i = 0; i < n; i++) {
stack->array[i] = i % 255;
}
Write_Mc_Stack("../data/test.tif", stack, NULL);
#endif
#if 0 /* test reading large stack */
Mc_Stack *stack = Read_Mc_Stack("../data/test.tif", -1);
Print_Mc_Stack_Info(stack);
#endif
#if 0 /* test writing a raw stack */
Mc_Stack *stack = Read_Mc_Stack("/Users/zhaot/Data/SynapseSpotted2_S124-3_1to59NF1Crop1_enhanced_Sample.tif", -1);
//Print_Stack_Info(stack);
Write_Mc_Stack("../data/test.raw", stack, NULL);
#endif
#if 0 /* test reading a raw stack */
/*
Stack *stack = Read_Raw_Stack("/Users/zhaot/Data/jinny/slice15_overplaped.raw");
Print_Stack_Info(stack);
Write_Stack("../data/test.tif", stack);
*/
Stack *stack = Read_Sc_Stack("/Users/zhaot/Data/jinny/proofread_slice15_3to11/detectedresults/slice15_3to11_crop01_detected_test.raw", 1);
Print_Stack_Info(stack);
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Stack *stack = Read_Sc_Stack("/Users/zhaot/Data/jinny/drawMask/slice15_3to33_4_30_result.raw", 2);
stack = Read_Stack_U("/Users/zhaot/Data/jinny/drawMask/slice15_3to33.raw");
#endif
#if 0
Stack *stack =
Read_Stack_U("/Users/zhaot/Work/neurolabi/data/diadem_d1_095.xml");
Print_Stack_Info(stack);
#endif
#if 0
Stack *stack =
Read_Stack_U("/Users/zhaot/Work/neurolabi/data/diadem_d1_001.xml");
Print_Stack_Info(stack);
Mc_Stack *mc_stack = Mc_Stack_Rewrap_Stack(stack);
printf("%d\n", Stack_Usage());
printf("%d\n", Mc_Stack_Usage());
Print_Mc_Stack_Info(mc_stack);
Write_Mc_Stack("../data/test.tif", mc_stack, NULL);
Free_Mc_Stack(mc_stack);
mc_stack = Read_Mc_Stack("/Users/zhaot/Work/neurolabi/data/diadem_d1_001.xml", -1);
printf("%d\n", Mc_Stack_Usage());
#endif
#if 0
int size[3];
Stack_Size_F("../data/benchmark/L3_12bit.lsm", size);
iarray_print2(size, 3, 1);
#endif
#if 0
Mc_Stack *stack =
Read_Mc_Stack("/Users/zhaot/Data/Julie/All_tiled_nsyb5_Sum.lsm", -1);
Print_Mc_Stack_Info(stack);
Write_Mc_Stack("../data/test.lsm", stack,
"/Users/zhaot/Data/Julie/All_tiled_nsyb5_Sum.lsm");
#endif
#if 0
Mc_Stack *stack =
Read_Mc_Stack("../data/test.lsm", -1);
Print_Mc_Stack_Info(stack);
#endif
#if 0
Mc_Stack *stack = NULL;
stack = Read_Mc_Stack("/Users/zhaot/Data/colorsep/16D01.1-14.lsm", 0);
Write_Mc_Stack("/Users/zhaot/Data/colorsep/channel1.tif", stack, NULL);
stack = Read_Mc_Stack("/Users/zhaot/Data/colorsep/16D01.1-14.lsm", 1);
Write_Mc_Stack("/Users/zhaot/Data/colorsep/channel2.tif", stack, NULL);
stack = Read_Mc_Stack("/Users/zhaot/Data/colorsep/16D01.1-14.lsm", 2);
Write_Mc_Stack("/Users/zhaot/Data/colorsep/channel3.tif", stack, NULL);
stack = Read_Mc_Stack("/Users/zhaot/Data/colorsep/16D01.1-14.lsm", 3);
Write_Mc_Stack("/Users/zhaot/Data/colorsep/channel4.tif", stack, NULL);
/*
Write_Mc_Stack("../data/test.lsm", stack,
"/Users/zhaot/Data/Julie/All_tiled_nsyb5_Sum.lsm");
*/
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("/Users/zhaot/Data/colorsep/16D01.1-14.lsm",
-1);
Print_Mc_Stack_Info(stack);
Stack grey_stack = Mc_Stack_Channel(stack, 3);
grey_stack.text = "\0";
Write_Stack("../data/test.tif", &grey_stack);
#endif
#if 0
printf("Channel number: %d\n", Lsm_Channel_Number("../data/12bit/70208_2BcPhR_R1_GR1_B1_L003.lsm"));
printf("Image type:");
switch (Lsm_Pixel_Type("../data/12bit/70208_2BcPhR_R1_GR1_B1_L003.lsm")) {
case GREY8:
printf(" uint8\n");
break;
case GREY16:
printf(" uint16\n");
break;
case FLOAT32:
printf(" float32\n");
break;
default:
printf(" unknown\n");
}
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/brainbow/CA3.lsm", 0);
Print_Mc_Stack_Info(stack);
Write_Mc_Stack("../data/test.tif", stack, NULL);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/test.xml");
Write_Stack("../data/test.tif", stack);
#endif
#if 0
int width, height, depth, kind;
Tiff_Attribute("../data/stack8.tif", 0, &kind, &width, &height, &depth);
printf("%d %d %d %d\n", width, height, depth, kind);
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/neuronsep/Lee_Lab/13C01_BLM00090_D2.v3dpdb", 1);
Print_Mc_Stack_Info(stack);
Write_Mc_Stack("../data/test.tif", stack, NULL);
#endif
#if 0
//Mc_Stack *stack = Read_Mc_Stack("../data/benchmark/bfork_2d.tif", -1);
//Mc_Stack *stack = Read_Mc_Stack("../data/neuronsep/Lee_Lab/13C01_BLM00090_D2.v3dpdb", 0);
Mc_Stack *stack = Read_Mc_Stack("../data/neuronsep/stitched-1.v3dpdb", 0);
//stack->depth = 1;
Stack ch = Mc_Stack_Channel(stack, 0);
printf("%g\n", Stack_Sum(&ch));
int *hist = Stack_Hist(&ch);
Print_Int_Histogram(hist);
Print_Mc_Stack_Info(stack);
Write_Mc_Stack("../data/test.tif", stack, NULL);
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/neurosep/aljosha/stitched-1858872924438528098.v3draw", -1);
Print_Mc_Stack_Info(stack);
#endif
#if 1
IMatrix *mat = IMatrix_Read("../data/test/session2/body_map/body_map00161.imat");
printf("%d: %d x %d x %d\n", (int) mat->ndim, mat->dim[0], mat->dim[1],
mat->dim[2]);
Stack *stack = Make_Stack(GREY, mat->dim[0], mat->dim[1], mat->dim[2]);
size_t nvoxel = Stack_Voxel_Number(stack);
for (size_t i = 0; i < nvoxel; ++i) {
stack->array[i] = (mat->array[i]) >> 24;
}
Write_Stack("../data/test.tif", stack);
#endif
return 0;
}
int main(int argc, char* argv[]) {
char neuron_name[100];
if (argc == 1) {
strcpy(neuron_name, "fly_neuron");
} else {
strcpy(neuron_name, argv[1]);
}
char file_path[100];
sprintf(file_path, "../data/%s.tif", neuron_name);
Stack *stack = Read_Stack(file_path);
int nvoxel = Stack_Voxel_Number(stack);
/* 1.5GB for double */
if (nvoxel < iround(962592768.0 / (8.0 + stack->kind))) {
DMatrix *filter = Mexihat_2D_D(2.0, NULL);
filter->ndim = 3;
filter->dim[2] = 1;
DMatrix *out = Filter_Stack_Fast_D(stack, filter, NULL, 0);
Kill_Stack(stack);
Kill_DMatrix(filter);
stack = Scale_Double_Stack(out->array, out->dim[0], out->dim[1],
out->dim[2], GREY);
Kill_DMatrix(out);
} else {
printf("Large volume data. Float version activated.\n");
FMatrix *filter = Mexihat_2D_F(2.0, NULL);
filter->ndim = 3;
filter->dim[2] = 1;
FMatrix *out = Filter_Stack_Fast_F(stack, filter, NULL, 0);
Kill_Stack(stack);
Kill_FMatrix(filter);
stack = Scale_Float_Stack(out->array, out->dim[0], out->dim[1],
out->dim[2], GREY);
Kill_FMatrix(out);
}
sprintf(file_path, "../data/%s/highpass.tif", neuron_name);
Write_Stack(file_path, stack);
printf("%s created.\n", file_path);
Kill_Stack(stack);
/*
DMatrix_Negative(out);
stack = Scale_Double_Stack(out->array, out->dim[0], out->dim[1],
out->dim[2], GREY16);
*/
//Stack_View sv = Stack_View_DMatrix(out);
/*
Stack *locmax = Stack_Local_Max(stack, NULL, STACK_LOCMAX_NONFLAT);
sprintf(file_path, "../data/%s/highpass_locmin.tif", neuron_name);
Write_Stack(file_path, locmax);
printf("%s created.\n", file_path);
Kill_Stack(locmax);
*/
return 0;
}
int main()
{
#if 0
char *filepath = "../data/fly_neuron_n2/graph_d.swc";
Neuron_Structure *ns = Neuron_Structure_From_Swc_File(filepath);
Neuron_Component_Arraylist *comp_array =
Neuron_Structure_Branch_Point(ns);
filepath = "../data/fly_neuron_n2.tif";
Stack *stack = Read_Stack(filepath);
Translate_Stack(stack, COLOR, 1);
int i;
Stack_Draw_Workspace *ws = New_Stack_Draw_Workspace();
for (i = 0; i < comp_array->length; i++) {
Neuron_Component_Draw_Stack(comp_array->array + i, stack, ws);
}
Kill_Stack_Draw_Workspace(ws);
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Stack *stack = NULL;
Locseg_Chain *chain1 = Read_Locseg_Chain("../data/fly_neuron_n3/chain0.tb");
Locseg_Chain *chain2 = Read_Locseg_Chain("../data/fly_neuron_n3/chain10.tb");
Connection_Test_Workspace *ws = New_Connection_Test_Workspace();
Connection_Test_Workspace_Read_Resolution(ws, "../data/fly_neuron_n1.res");
Neurocomp_Conn conn;
conn.mode = NEUROCOMP_CONN_HL;
Locseg_Chain_Connection_Test(chain1, chain2, stack, 1.0, &conn, ws);
Print_Neurocomp_Conn(&conn);
#endif
#if 0
Locseg_Chain **chain = (Locseg_Chain**) malloc(sizeof(Locseg_Chain*) * 3);
chain[0] = Read_Locseg_Chain("../data/mouse_single_org/chain4.tb");
chain[1] = Read_Locseg_Chain("../data/mouse_single_org/chain19.tb");
chain[2] = Read_Locseg_Chain("../data/mouse_single_org/chain64.tb");
Stack *signal = Read_Stack("../data/mouse_single_org.tif");
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
FILE *fp = fopen("../data/mouse_single_org.res", "r");
darray_fscanf(fp, ctw->resolution, 3);
Neuron_Component *chain_array = Make_Neuron_Component_Array(3);
int i;
for (i = 0; i < 3; i++) {
Set_Neuron_Component(chain_array + i,
NEUROCOMP_TYPE_LOCSEG_CHAIN, chain[i]);
}
Neuron_Structure *ns = Locseg_Chain_Comp_Neurostruct(chain_array,
3, signal, 1.0, ctw);
Graph *graph = ns->graph;
Process_Neuron_Structure(ns);
Print_Neuron_Structure(ns);
Neuron_Structure_Crossover_Test(ns, 0.5375);
printf("\ncross over changed: \n");
Print_Neuron_Structure(ns);
#endif
#if 0
Neuron_Structure *ns = Make_Neuron_Structure(5);
Set_Neuron_Component(ns->comp, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 1, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 2, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 3, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
Set_Neuron_Component(ns->comp + 4, NEUROCOMP_TYPE_GEO3D_CIRCLE,
New_Geo3d_Circle());
NEUROCOMP_GEO3D_CIRCLE(ns->comp)->radius = 1.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 1)->radius = 2.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 2)->radius = 3.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 3)->radius = 4.5;
NEUROCOMP_GEO3D_CIRCLE(ns->comp + 4)->radius = 5.5;
ns->graph = Make_Graph(5, 4, 0);
//Graph_Add_Edge(ns->graph, 0, 1);
Graph_Add_Edge(ns->graph, 1, 3);
Graph_Add_Edge(ns->graph, 1, 4);
Graph_Add_Edge(ns->graph, 0, 2);
Graph_Set_Directed(ns->graph, TRUE);
Print_Graph(ns->graph);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns, 1.0, NULL);
Print_Swc_Tree(tree);
Swc_Tree_To_Dot_File(tree, "../data/test2.dot");
#endif
#if 0
int n;
Neuron_Component *chain_array = Dir_Locseg_Chain_Nc("../data/fly_neuron_n22",
"^chain.*\\.tb",
&n, NULL);
Neuron_Structure *ns =
Locseg_Chain_Comp_Neurostruct(chain_array, n, NULL, 1.0, NULL);
Process_Neuron_Structure(ns);
Neuron_Structure* ns2=
Neuron_Structure_Locseg_Chain_To_Circle(ns);
Neuron_Structure_To_Tree(ns2);
Graph_To_Dot_File(ns2->graph, "../data/test.dot");
Swc_Tree *tree =
Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
Swc_Tree_Remove_Zigzag(tree);
//Swc_Tree_Tune_Fork(tree);
//Print_Swc_Tree(tree);
Write_Swc_Tree("../data/test.swc", tree);
#endif
#if 0
Graph *graph = Neuron_Structure_Import_Xml_Graph("../data/mouse_single_org/trueconn2.xml");
Graph_Normalize_Edge(graph);
Graph_Remove_Duplicated_Edge(graph);
Graph *graph2 = Neuron_Structure_Import_Xml_Graph("../data/mouse_single_org/conn.xml");
Graph_Normalize_Edge(graph2);
Graph_Remove_Duplicated_Edge(graph2);
Graph_Workspace *gw = New_Graph_Workspace();
int n = Graph_Edge_Count(graph, graph2->edges, graph2->nedge, gw);
printf("fp: %d\n", graph2->nedge - n);
printf("tp: %d\n", n);
printf("fn: %d\n", graph->nedge - n);
double p = (double) n / graph2->nedge;
double r = (double) n / graph->nedge;
printf("precision: %g\n", p);
printf("recall: %g\n", r);
printf("F-measure: %g\n", 2.0 * (p * r) / (p + r));
#endif
#if 0
Neuron_Structure *ns = Make_Neuron_Structure(2);
Local_Neuroseg *locseg = New_Local_Neuroseg();
Locseg_Chain *chain1 = New_Locseg_Chain();
Locseg_Chain_Add(chain1, locseg, NULL, DL_TAIL);
Set_Neuron_Component(ns->comp, NEUROCOMP_TYPE_LOCSEG_CHAIN, chain1);
Locseg_Chain *chain2 = New_Locseg_Chain();
locseg = New_Local_Neuroseg();
double bottom[3] = {10, 10, 5};
double top[3] = {5, 5, 5};
Local_Neuroseg_Set_Bottom_Top(locseg, bottom, top);
Locseg_Chain_Add(chain2, locseg, NULL, DL_TAIL);
Set_Neuron_Component(ns->comp + 1, NEUROCOMP_TYPE_LOCSEG_CHAIN, chain2);
Neurocomp_Conn *conn = New_Neurocomp_Conn();
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
Locseg_Chain_Connection_Test(chain2, chain1, NULL, 1.0, conn, ctw);
Neuron_Structure_Add_Conn(ns, 1, 0, conn);
Print_Neuron_Structure(ns);
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Neuron_Structure_To_Swc_File(ns2, "../data/test.swc");
#endif
#if 0
int n;
Locseg_Chain **chain_array = Dir_Locseg_Chain_Nd("../data/diadem_a1_part3",
"^chain.*\\.tb", &n, NULL);
/*
Locseg_Chain **chain_array =
Locseg_Chain_Import_List("../data/diadem_a1_part2/good_tube.txt", &n);
*/
//n = 100;
/*
Locseg_Chain **chain_array =
(Locseg_Chain**) malloc(sizeof(Locseg_Chain*) * 2);
n = 2;
chain_array[0] = Read_Locseg_Chain("../data/diadem_a1_part2/chain58.tb");
chain_array[1] = Read_Locseg_Chain("../data/diadem_a1_part2/chain154.tb");
*/
Stack *stack = Read_Stack("../data/diadem_a1_part3.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
sgw->resolution[0] = 0.0375 * 2.0;
sgw->resolution[1] = 0.0375 * 2.0;
sgw->resolution[2] = 0.33;
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Print_Neuron_Structure(ns);
Graph_To_Dot_File(ns->graph, "../data/test.dot");
//Neuron_Structure_To_Swc_File(ns, "../data/test.swc");
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
//double root[3] = {31, 430, 0};
double root[3] = {1221, 449, 8.5};
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, root);
Swc_Tree_Clean_Root(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test.swc", tree);
#endif
#if 0
int n;
Locseg_Chain **chain_array = Dir_Locseg_Chain_Nd("../data/diadem_e1",
"^chain.*\\.tb", &n, NULL);
//n = 100;
/*
Locseg_Chain **chain_array =
(Locseg_Chain**) malloc(sizeof(Locseg_Chain*) * 2);
n = 2;
chain_array[0] = Read_Locseg_Chain("../data/diadem_a1_part2/chain58.tb");
chain_array[1] = Read_Locseg_Chain("../data/diadem_a1_part2/chain154.tb");
*/
Stack *stack = Read_Stack("../data/diadem_e1.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
sgw->resolution[0] = 0.3296485;
sgw->resolution[1] = 0.3296485;
sgw->resolution[2] = 1.0;
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Print_Neuron_Structure(ns);
//Neuron_Structure_To_Swc_File(ns, "../data/test.swc");
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Graph_To_Dot_File(ns2->graph, "../data/test.dot");
double root[3] = {31, 430, 0};
//double root[3] = {4882, 1797, 19};
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, root);
//Swc_Tree_Clean_Root(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test2.swc", tree);
#endif
#if 0
int n;
Locseg_Chain **chain_array =
Dir_Locseg_Chain_Nd("../data/benchmark/stack_graph/fork", "^chain.*\\.tb",
&n, NULL);
Stack *stack = Read_Stack("../data/benchmark/stack_graph/fork/fork.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
//Swc_Tree_Clean_Root(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test.swc", tree);
#endif
#if 0
int n = 3;
Locseg_Chain **chain_array =
(Locseg_Chain**) malloc(sizeof(Locseg_Chain) * n);
chain_array[0] = Read_Locseg_Chain("/Users/zhaot/Work/neurolabi/data/benchmark/stack_graph/fork/chain0.tb");
chain_array[1] = Read_Locseg_Chain("/Users/zhaot/Work/neurolabi/data/benchmark/stack_graph/fork/chain1.tb");
chain_array[2] = New_Locseg_Chain();
printf("%d\n", Locseg_Chain_Is_Empty(chain_array[2]));
Stack *stack = Read_Stack("../data/benchmark/stack_graph/fork/fork.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Neuron_Structure *ns2 =
Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
//Swc_Tree_Clean_Root(tree);
Swc_Tree_Remove_Zigzag(tree);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test2.swc", tree);
#endif
#if 0
Neuron_Structure *ns = New_Neuron_Structure();
ns->graph = New_Graph();
Graph_Add_Edge(ns->graph, 0, 1);
Graph_Add_Edge(ns->graph, 0, 2);
Graph_Add_Edge(ns->graph, 2, 3);
Graph_Add_Edge(ns->graph, 2, 4);
Graph_Add_Edge(ns->graph, 4, 5);
Graph_Add_Edge(ns->graph, 5, 6);
ns->conn = (Neurocomp_Conn*) malloc(sizeof(Neurocomp_Conn) * ns->graph->nedge);
ns->conn[0].info[0] = 0;
ns->conn[0].info[1] = 0;
ns->conn[0].cost = 0.0;
ns->conn[0].mode = NEUROCOMP_CONN_LINK;
ns->conn[1].info[0] = 1;
ns->conn[1].info[1] = 1;
ns->conn[1].cost = 0.0;
ns->conn[1].mode = NEUROCOMP_CONN_LINK;
ns->conn[2].info[0] = 0;
ns->conn[2].info[1] = 0;
ns->conn[2].cost = 0.0;
ns->conn[2].mode = NEUROCOMP_CONN_LINK;
ns->conn[3].info[0] = 1;
ns->conn[3].info[1] = 0;
ns->conn[3].cost = 1.0;
ns->conn[3].mode = NEUROCOMP_CONN_HL;
ns->conn[4].info[0] = 0;
ns->conn[4].info[1] = 1;
ns->conn[4].cost = 0.0;
ns->conn[4].mode = NEUROCOMP_CONN_LINK;
ns->conn[5].info[0] = 1;
ns->conn[5].info[1] = 1;
ns->conn[5].cost = 1.0;
ns->conn[5].mode = NEUROCOMP_CONN_LINK;
Neuron_Structure_Merge_Locseg_Chain(ns);
#endif
#if 0
Neuron_Structure *ns = New_Neuron_Structure();
ns->graph = New_Graph();
ns->comp = Dir_Locseg_Chain_Nc("../data/diadem_e3", "^chain.*\\.tb",
&(ns->graph->nvertex), NULL);
Graph_Add_Edge(ns->graph, 0, 1);
Graph_Add_Edge(ns->graph, 0, 2);
Graph_Add_Edge(ns->graph, 2, 3);
Graph_Add_Edge(ns->graph, 3, 4);
Graph_Add_Edge(ns->graph, 4, 5);
ns->conn = (Neurocomp_Conn*) malloc(sizeof(Neurocomp_Conn) * ns->graph->nedge);
ns->conn[0].info[0] = 0;
ns->conn[0].info[1] = 0;
ns->conn[0].cost = 0.0;
ns->conn[0].mode = NEUROCOMP_CONN_LINK;
ns->conn[1].info[0] = 0;
ns->conn[1].info[1] = 0;
ns->conn[1].cost = 0.0;
ns->conn[1].mode = NEUROCOMP_CONN_LINK;
ns->conn[2].info[0] = 0;
ns->conn[2].info[1] = 0;
ns->conn[2].cost = 1.0;
ns->conn[2].mode = NEUROCOMP_CONN_LINK;
ns->conn[3].info[0] = 0;
ns->conn[3].info[1] = 0;
ns->conn[3].cost = 2.0;
ns->conn[3].mode = NEUROCOMP_CONN_LINK;
ns->conn[4].info[0] = 0;
ns->conn[4].info[1] = 0;
ns->conn[4].cost = 0.0;
ns->conn[4].mode = NEUROCOMP_CONN_LINK;
int i;
for (i = 0; i < ns->graph->nvertex; i++) {
printf("%d ", Locseg_Chain_Length(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i)));
}
printf("\n");
Neuron_Structure_Merge_Locseg_Chain(ns);
for (i = 0; i < ns->graph->nvertex; i++) {
printf("%d ", Locseg_Chain_Length(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i)));
}
printf("\n");
#endif
#if 0
int n;
Locseg_Chain **chain_array = Dir_Locseg_Chain_Nd("../data/diadem_e1",
"^chain.*\\.tb", &n, NULL);
Stack *stack = Read_Stack("../data/diadem_e1.tif");
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
Zero_Stack(mask);
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = Stack_Voxel_Number(stack);
sgw->resolution[0] = 0.3296485;
sgw->resolution[1] = 0.3296485;
sgw->resolution[2] = 1.0;
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_S;
Stack_Sp_Grow_Infer_Parameter(sgw, stack);
Neuron_Structure *ns =
Locseg_Chain_Sp_Grow_Reconstruct(chain_array, n, stack, 1.0, sgw);
Neuron_Structure_Merge_Locseg_Chain(ns);
int i;
char filepath[100];
for (i = 0; i < ns->graph->nvertex; i++) {
Locseg_Chain_Regularize(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i));
if (Locseg_Chain_Is_Empty(NEUROCOMP_LOCSEG_CHAIN(ns->comp+i)) == FALSE) {
sprintf(filepath, "../data/tmp/chain%d.tb", i);
Write_Locseg_Chain(filepath, NEUROCOMP_LOCSEG_CHAIN(ns->comp+i));
}
}
#endif
#if 0
Stack *stack = Read_Stack("../data/benchmark/fork2/fork2.tif");
Neuron_Structure *ns = New_Neuron_Structure();
ns->graph = New_Graph();
ns->comp = Dir_Locseg_Chain_Nc("../data/benchmark/fork2/tubes",
"^chain.*\\.tb", &(ns->graph->nvertex), NULL);
coordinate_3d_t roots[3];
roots[0][0] = 51;
roots[0][1] = 23;
roots[0][2] = 60;
roots[1][0] = 51;
roots[1][1] = 23;
roots[1][2] = 40;
roots[2][0] = 25;
roots[2][1] = 76;
roots[2][2] = 60;
Neuron_Structure_Break_Root(ns, roots, 3);
Neuron_Structure_Load_Root(ns, roots, 3);
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
ctw->dist_thre = 100.0;
ctw->sp_test = FALSE;
Locseg_Chain_Comp_Neurostruct_W(ns, stack, 1.0, ctw);
Process_Neuron_Structure(ns);
Neuron_Structure_To_Tree(ns);
/*
Neuron_Structure_Remove_Conn(ns, 0, 2);
Neuron_Structure_Remove_Conn(ns, 2, 0);
*/
Neuron_Structure_Remove_Negative_Conn(ns);
Neuron_Structure* ns2= NULL;
ns2 = Neuron_Structure_Locseg_Chain_To_Circle_S(ns, 1.0, 1.0);
Neuron_Structure_To_Tree(ns2);
Swc_Tree *tree = Neuron_Structure_To_Swc_Tree_Circle_Z(ns2, 1.0, NULL);
Swc_Tree_Resort_Id(tree);
Write_Swc_Tree("../data/test3.swc", tree);
#endif
#if 1
Stack *stack = NULL;
Locseg_Chain *chain1 = Read_Locseg_Chain("../data/benchmark/diadem/diadem_e1/chain22.tb");
Locseg_Chain *chain2 = Read_Locseg_Chain("../data/benchmark/diadem/diadem_e1/chain0.tb");
Connection_Test_Workspace *ws = New_Connection_Test_Workspace();
Connection_Test_Workspace_Read_Resolution(ws, "../data/diadem_e3.res");
Neurocomp_Conn conn;
conn.mode = NEUROCOMP_CONN_HL;
Locseg_Chain_Connection_Test(chain1, chain2, stack, 1.0, &conn, ws);
Print_Neurocomp_Conn(&conn);
#endif
return 0;
}
int main(int argc, char *argv[])
{
static char *Spec[] = {"[-z <double>]", NULL};
Process_Arguments(argc, argv, Spec, 1);
#if 0
Locseg_Chain *chain1 = Read_Locseg_Chain("../data/ct017/test5/chain2.bn");
Locseg_Chain *chain2 = Read_Locseg_Chain("../data/ct017/test5/chain1.bn");
if (Is_Arg_Matched("-z")) {
double z_scale = Get_Double_Arg("-z");
Locseg_Chain_Scale_Z(chain1, z_scale);
Locseg_Chain_Scale_Z(chain2, z_scale);
}
Neurocomp_Conn conn;
Locseg_Chain_Connection_Test_P(chain1, chain2, &conn);
Print_Neurocomp_Conn(&conn);
double scale = 2.0;
double offset = 5.0;
Local_Neuroseg *locseg1;
if (conn.info[0] == 0) {
locseg1 = Locseg_Chain_Head_Seg(chain1);
Local_Neuroseg_Stretch(locseg1, scale, offset, -1);
} else {
locseg1 = Locseg_Chain_Tail_Seg(chain1);
Local_Neuroseg_Stretch(locseg1, scale, offset, 1);
}
Local_Neuroseg *locseg2 = Locseg_Chain_Peek_Seg_At(chain2, conn.info[1]);
Local_Neuroseg_Stretch(locseg2, scale, offset, 0);
printf("%g\n", Local_Neuroseg_Planar_Dist_L(locseg1, locseg2));
FILE *fp = fopen("../data/ct017/test5/test.swc", "w");
/* to avoid v3d bug */
Local_Neuroseg *tmp_locseg = Copy_Local_Neuroseg(locseg1);
tmp_locseg->seg.r1 = 0.1;
Local_Neuroseg_Swc_Fprint(fp, tmp_locseg, 0, -1);
Local_Neuroseg_Swc_Fprint(fp, locseg1, 2, -1);
Local_Neuroseg_Swc_Fprint(fp, locseg2, 4, -1);
fclose(fp);
Locseg_Chain_Connection_Test(chain1, chain2, NULL, 1.0, &conn, NULL);
Print_Neurocomp_Conn(&conn);
#endif
#if 0
double z_scale = 0.5375;
Locseg_Chain *chain[11];
char file_path[100];
int i, j;
for (i = 0; i < 11; i++) {
sprintf(file_path, "../data/mouse_single_org/chain%d.bn", i);
chain[i] = Read_Locseg_Chain(file_path);
Locseg_Chain_Scale_Z(chain[i], z_scale);
}
Neurocomp_Conn conn;
for (i = 0; i < 11; i++) {
for (j = 0; j < 11; j++) {
if (i != j) {
if (Locseg_Chain_Connection_Test_P(chain[i], chain[j], &conn) < 5.0) {
printf("%d -> %d \n", i, j);
Print_Neurocomp_Conn(&conn);
}
}
}
}
#endif
#if 0
double z_scale = 0.5375;
int n = 278;
Locseg_Chain *chain[n];
char file_path[100];
int i, j;
for (i = 0; i < n; i++) {
sprintf(file_path, "../data/mouse_single_org/chain%d.bn", i);
chain[i] = Read_Locseg_Chain(file_path);
Locseg_Chain_Scale_Z(chain[i], z_scale);
}
Locseg_Chain *hook = chain[19];
Neurocomp_Conn conn;
for (i = 0; i < n; i++) {
if (i != 19) {
if (Locseg_Chain_Connection_Test_P(hook, chain[i], &conn) < 5.0) {
printf("19 -> %d \n", i);
Print_Neurocomp_Conn(&conn);
}
}
}
#endif
#if 0
double z_scale = 0.32;
Locseg_Chain *chain[17];
char file_path[100];
int i, j;
for (i = 0; i < 17; i++) {
sprintf(file_path, "../data/fly_neuron_n1/chain%d.bn", i);
chain[i] = Read_Locseg_Chain(file_path);
Locseg_Chain_Scale_Z(chain[i], z_scale);
}
Neurocomp_Conn conn;
for (i = 0; i < 17; i++) {
for (j = 0; j < 17; j++) {
if (i != j) {
if (Locseg_Chain_Connection_Test_P(chain[i], chain[j], &conn) < 5.0) {
printf("%d -> %d \n", i, j);
Print_Neurocomp_Conn(&conn);
}
}
}
}
#endif
#if 0
double z_scale = 0.1400;
//double z_scale = 1.0;
int n = 12;
Locseg_Chain *chain[n];
char file_path[100];
int i, j;
for (i = 0; i < n; i++) {
sprintf(file_path, "../data/ct017/test6/chain%d.bn", i);
chain[i] = Read_Locseg_Chain(file_path);
Locseg_Chain_Scale_Z(chain[i], z_scale);
}
Neurocomp_Conn conn;
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
if (i != j) {
if (Locseg_Chain_Connection_Test_P(chain[i], chain[j], &conn) < 10.0) {
printf("%d -> %d \n", i, j);
Print_Neurocomp_Conn(&conn);
}
}
}
}
#endif
#if 0
//double z_scale = 0.1400;
double z_scale = 1.20;
int n = 5;
Locseg_Chain *chain[n];
char file_path[100];
int i, j;
for (i = 0; i < n; i++) {
sprintf(file_path, "../data/ct017/test7/chain%d.bn", i);
chain[i] = Read_Locseg_Chain(file_path);
Locseg_Chain_Scale_Z(chain[i], z_scale);
}
Neurocomp_Conn conn;
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
if (i != j) {
if (Locseg_Chain_Connection_Test_P(chain[i], chain[j], &conn) < 10.0) {
printf("%d -> %d \n", i, j);
Print_Neurocomp_Conn(&conn);
}
}
}
}
#endif
#if 0
double z_scale = 1.20;
//double z_scale = 1.0;
Stack *stack = Read_Stack("../data/lobster_neuron_org.tif");
int n = 5;
Locseg_Chain *chain[n];
char file_path[100];
int i, j;
for (i = 0; i < n; i++) {
sprintf(file_path, "../data/ct017/test7/chain%d.bn", i);
chain[i] = Read_Locseg_Chain(file_path);
//Locseg_Chain_Scale_Z(chain[i], z_scale);
}
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
ctw->z_scale = z_scale;
Neurocomp_Conn conn;
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
if (i != j) {
if (Locseg_Chain_Connection_Test(chain[i], chain[j], stack, 1.0,
&conn, ctw)) {
printf("%d -> %d \n", i, j);
Print_Neurocomp_Conn(&conn);
}
}
}
}
#endif
#if 0
Locseg_Chain *chain = Read_Locseg_Chain("../data/ct017/test6/chain7.bn");
Local_Neuroseg *locseg = Locseg_Chain_Tail_Seg(chain);
Print_Local_Neuroseg(locseg);
Stack *stack = Read_Stack("../data/mouse_neuron_sp2.tif");
double *profile = Local_Neuroseg_Height_Profile(locseg, stack, 1.0,
11, STACK_FIT_CORRCOEF,
NULL);
darray_write("../data/profile1.bn", profile, 11);
#endif
#if 0
Locseg_Chain *chain = Read_Locseg_Chain("../data/ct017/test6/chain7.bn");
Local_Neuroseg *locseg = Locseg_Chain_Tail_Seg(chain);
Print_Local_Neuroseg(locseg);
Stack *stack = Read_Stack("../data/mouse_neuron_sp2.tif");
int n;
double record[11];
Locseg_Chain *chain2 = Local_Neuroseg_Push(locseg, stack,
1.0, STACK_FIT_OUTER_SIGNAL,
record, &n);
Print_Locseg_Chain(chain2);
Write_Locseg_Chain("../data/test.tb", chain2);
return 1;
Locseg_Chain *chain3 = Read_Locseg_Chain("../data/ct017/test6/chain6.bn");
Locseg_Chain_Scale_Z(chain2, 0.14);
Locseg_Chain_Scale_Z(chain3, 0.14);
Neurocomp_Conn conn;
Locseg_Chain_Connection_Test(chain2, chain3, NULL, 1.0, &conn, NULL);
Print_Neurocomp_Conn(&conn);
#endif
#if 0
Locseg_Chain *chain = Read_Locseg_Chain("../data/ct017/test6/chain9.bn");
Local_Neuroseg *locseg = Locseg_Chain_Tail_Seg(chain);
//Local_Neuroseg *locseg = Locseg_Chain_Head_Seg(chain);
//Flip_Local_Neuroseg(locseg);
Print_Local_Neuroseg(locseg);
Stack *stack = Read_Stack("../data/mouse_neuron_sp2.tif");
int n;
double record[11];
Locseg_Chain *chain2 = Local_Neuroseg_Push(locseg, stack,
1.0, STACK_FIT_OUTER_SIGNAL,
record, &n);
Print_Locseg_Chain(chain2);
Write_Locseg_Chain("../data/test.bn", chain2);
return 1;
Locseg_Chain *chain3 = Read_Locseg_Chain("../data/ct017/test6/chain9.bn");
Locseg_Chain_Scale_Z(chain2, 0.14);
Locseg_Chain_Scale_Z(chain3, 0.14);
Neurocomp_Conn conn;
Locseg_Chain_Connection_Test(chain3, chain2, stack, 1.0, &conn, NULL);
Print_Neurocomp_Conn(&conn);
#endif
#if 0
double z_scale = 0.1400;
//double z_scale = 1.0;
Stack *stack = Read_Stack("../data/mouse_neuron_sp2.tif");
int n = 12;
Locseg_Chain *chain[n];
char file_path[100];
int i, j;
for (i = 0; i < n; i++) {
sprintf(file_path, "../data/ct017/test6/chain%d.bn", i);
chain[i] = Read_Locseg_Chain(file_path);
//Locseg_Chain_Scale_Z(chain[i], z_scale);
}
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
ctw->z_scale = 0.14;
Neurocomp_Conn conn;
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
if (i != j) {
if (Locseg_Chain_Connection_Test(chain[i], chain[j], stack, 1.0,
&conn, ctw)) {
printf("%d -> %d \n", i, j);
Print_Neurocomp_Conn(&conn);
}
}
}
}
#endif
#if 0
//double z_scale = 0.32;
//double z_scale = 1.0;
Stack *stack = Read_Stack("../data/fly_neuron_n1.tif");
int n = 17;
Locseg_Chain *chain[n];
char file_path[100];
int i, j;
for (i = 0; i < n; i++) {
sprintf(file_path, "../data/fly_neuron_n1/chain%d.tb", i);
chain[i] = Read_Locseg_Chain(file_path);
//Locseg_Chain_Scale_Z(chain[i], z_scale);
}
Connection_Test_Workspace *ctw = New_Connection_Test_Workspace();
ctw->resolution[0] = 0.32;
ctw->resolution[1] = 0.32;
ctw->resolution[2] = 1.0;
Neurocomp_Conn conn;
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
if (i != j) {
if (Locseg_Chain_Connection_Test(chain[i], chain[j], stack, 1.0,
&conn, ctw)) {
printf("%d -> %d \n", i, j);
Print_Neurocomp_Conn(&conn);
}
}
}
}
#endif
#if 0
Locseg_Chain *chain = Read_Locseg_Chain("../data/fly_neuron_n1/chain3.bn");
Local_Neuroseg *locseg = Locseg_Chain_Tail_Seg(chain);
//Flip_Local_Neuroseg(locseg);
Print_Local_Neuroseg(locseg);
Stack *stack = Read_Stack("../data/fly_neuron_n1.tif");
int n;
double record[11];
Locseg_Chain *chain2 = Local_Neuroseg_Push(locseg, stack,
1.0, STACK_FIT_CORRCOEF,
record, &n);
Print_Locseg_Chain(chain2);
Write_Locseg_Chain("../data/test.bn", chain2);
return 1;
Locseg_Chain *chain3 = Read_Locseg_Chain("../data/fly_neuron_n1/chain0.bn");
Locseg_Chain_Scale_Z(chain2, 0.32);
Locseg_Chain_Scale_Z(chain3, 0.32);
Neurocomp_Conn conn;
Locseg_Chain_Connection_Test(chain2, chain3, stack, 1.0, &conn, NULL);
Print_Neurocomp_Conn(&conn);
#endif
return 0;
}
int main(int argc, char *argv[])
{
static char *Spec[] = {"<input:string> -o <string>",
"[-count <int>] [-dist <int>] [-minobj <int>]", NULL};
Process_Arguments(argc, argv, Spec, 1);
Stack *input = Read_Stack(Get_String_Arg("input"));
int nregion = Stack_Max(input, NULL);
int nvoxel = Stack_Voxel_Number(input);
int i;
Stack *stack = Make_Stack(GREY, Stack_Width(input), Stack_Height(input),
Stack_Depth(input));
Stack *out = Make_Stack(GREY, Stack_Width(input), Stack_Height(input),
Stack_Depth(input));
Zero_Stack(out);
int nobj = 0;
for (i = 1; i <= nregion; i++) {
int j;
int count = 0;
for (j = 0; j < nvoxel; j++) {
stack->array[j] = (input->array[j] == i);
}
Stack *out3 = NULL;
int maxcount = 100000;
if (Is_Arg_Matched("-count")) {
maxcount = Get_Int_Arg("-count");
}
if (count > maxcount) {
out3 = Copy_Stack(stack);
Stack_Addc_M(out3, nobj);
nobj++;
} else {
Stack *distmap = Stack_Bwdist_L_U16P(stack, NULL, 0);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Copy_Stack(distmap);
int mindist = 10;
if (Is_Arg_Matched("-dist")) {
mindist = Get_Int_Arg("-dist");
}
Stack_Threshold_Binarize(ws->mask, mindist);
Translate_Stack(ws->mask, GREY, 1);
int minobj = 100;
if (Is_Arg_Matched("-minobj")) {
minobj = Get_Int_Arg("-minobj");
}
Object_3d_List *objs = Stack_Find_Object(ws->mask, 1, minobj);
Zero_Stack(ws->mask);
Stack_Draw_Objects_Bw(ws->mask, objs, -255);
ws->min_level = 1;
ws->start_level = 65535;
out3 = Stack_Watershed(distmap, ws);
Stack_Addc_M(out3, nobj);
nobj += Object_3d_List_Length(objs);
Kill_Stack(distmap);
Kill_Stack_Watershed_Workspace(ws);
Kill_Object_3d_List(objs);
}
Stack_Add(out, out3, out);
Kill_Stack(out3);
}
printf("number of regions: %d\n", nobj);
Write_Stack(Get_String_Arg("-o"), out);
char cmd[500];
sprintf(cmd, "touch %s_done", Get_String_Arg("-o"));
system(cmd);
return 0;
}
int main(int argc, char *argv[])
{
char puncta_swc_path[] = "/home/feng/otherSource/hand2.swc";
char puncta_meanshifted_swc_path[] = "/home/feng/otherSource/hand_meanshifted.swc";
char trace_result_path[] = "/home/feng/otherSource/015.trace/traced/";
char masked_swc_path[] = "/home/feng/otherSource/masked_hand.swc";
char masked_meanshifted_swc_path[] = "/home/feng/otherSource/masked_hand_meanshifted.swc";
char puncta_stack_path[] = "/home/feng/otherSource/C1-slice09_L5_Sum.tif";
int n;
Locseg_Chain* chains = Dir_Locseg_Chain_N(trace_result_path, "^chain[[:digit:]]*\\.tb", &n, NULL);
printf("found %d tb file\n", n);
int i=0;
Locseg_Label_Workspace* ws = New_Locseg_Label_Workspace();
Stack *mask = Make_Stack(GREY, 1024, 1024, 128);
Zero_Stack(mask);
double z_scale = 1;
double pixelperumxy = 9.66;
double pixelperumz = 2;
double maskextendbyum = 2.5;
double maskextendbypixel = maskextendbyum * pixelperumxy;
for (i=0; i<n; i++) {
Default_Locseg_Label_Workspace(ws);
ws->option = 1;
ws->sdiff = maskextendbypixel;
ws->value = 255;
Locseg_Chain_Label_W(&(chains[i]), mask, z_scale, 0, Locseg_Chain_Length(&(chains[i])), ws);
}
Write_Stack("/home/feng/otherSource/maskstack.tif", mask);
Swc_Node *punctas = Read_Swc_File(puncta_swc_path, &n);
printf("found %d puncta\n", n);
FILE *fp = fopen(masked_swc_path, "w");
for (i=0; i<n; i++) {
// if (*(STACK_PIXEL_8(mask, iround(punctas[i].x), iround(punctas[i].y), iround(punctas[i].z), 0)) == 255) {
// Swc_Node_Fprint(fp, &(punctas[i]));
// }
if (Stack_Neighbor_Mean(mask, 26, iround(punctas[i].x), iround(punctas[i].y), iround(punctas[i].z)) > 0) {
Swc_Node_Fprint(fp, &(punctas[i]));
}
}
fclose(fp);
fp = fopen(puncta_meanshifted_swc_path, "w");
Stack *puncta_stack = Read_Stack(puncta_stack_path);
for (i=0; i<n; i++) {
Geo3d_Ball *gb = New_Geo3d_Ball();
gb->center[0] = punctas[i].x;
gb->center[1] = punctas[i].y;
gb->center[2] = punctas[i].z;
gb->r = 3;
Geo3d_Ball_Mean_Shift(gb, puncta_stack, 1, 0.5);
punctas[i].x = gb->center[0];
punctas[i].y = gb->center[1];
punctas[i].z = gb->center[2];
Swc_Node_Fprint(fp, punctas+i);
Delete_Geo3d_Ball(gb);
}
fclose(fp);
Kill_Stack(puncta_stack);
fp = fopen(masked_meanshifted_swc_path, "w");
for (i=0; i<n; i++) {
if (Stack_Neighbor_Mean(mask, 26, iround(punctas[i].x), iround(punctas[i].y), iround(punctas[i].z)) > 0) {
Swc_Node_Fprint(fp, &(punctas[i]));
}
}
fclose(fp);
return 0;
}
int main(int argc, const char *argv[])
{
const char *dir_name = "/Users/zhaot/Data/nathan/2008-04-18";
if (argc > 1) {
dir_name = argv[1];
}
const char *result_dir = "/Users/zhaot/Work/V3D/neurolabi/data/align";
char filelist[100];
fullpath(result_dir, "filelist.txt", filelist);
printf("%s\n", filelist);
char file_path[150];
char image_path[150];
/* Read all files from the directory */
FILE *fp = fopen(filelist, "r");
char id[100];
int idx = 0;
int idx2 = 0;
int row = 22;
int col = 15;
#define MAX_FILE_NUMBER 364
char all_file[MAX_FILE_NUMBER][100];
double stack_mean[MAX_FILE_NUMBER];
int available[row * col];
while (Read_Word(fp, all_file[idx++], 0) > 0) {
fullpath(dir_name, all_file[idx - 1], image_path);
printf("%d, %s\n", idx, image_path);
}
fullpath(result_dir, "stack_mean.bn", file_path);
if (!fexist(file_path)) {
for (idx = 1; idx <= MAX_FILE_NUMBER; idx++) {
fullpath(dir_name, all_file[idx - 1], image_path);
Stack *stack = Read_Stack(image_path);
stack_mean[idx - 1] = Stack_Mean(stack);
printf("%d, %s: %g\n", idx, image_path, stack_mean[idx - 1]);
Kill_Stack(stack);
}
darray_write(file_path, stack_mean, MAX_FILE_NUMBER);
} else {
int array_length;
darray_read(file_path, stack_mean, &array_length);
}
if (idx - 1 != MAX_FILE_NUMBER) {
fprintf(stderr, "Wrong file number: %d.\n", idx);
}
const double threshold = 115.0;
for (idx = 0; idx < MAX_FILE_NUMBER; idx++) {
if (stack_mean[idx] > threshold) {
available[idx] = 1;
} else {
available[idx] = 0;
}
}
for (idx = MAX_FILE_NUMBER; idx < row * col; idx++) {
available[idx] = 0;
}
fullpath(result_dir, "align_input.txt", file_path);
fclose(fp);
int neighbor[] = {-1, 1, -22, 22};
fp = fopen(file_path, "w");
for (idx = 1; idx < MAX_FILE_NUMBER; idx++) {
if (idx % row != 0) {
if (available[idx - 1] && available[idx]) {
fprintf(fp, "%s %s\n", all_file[idx - 1], all_file[idx]);
align_id(all_file[idx - 1], all_file[idx], id);
printf("%s\n", id);
}
}
}
int i, j;
int offset = 0;
for (j = 0; j < col - 1; j++) {
offset = row * j;
for (i = 0; i < row; i++) {
idx = offset + i;
idx2 = idx + row;
if ((available[idx]) && (available[idx2])) {
fprintf(fp, "%s %s\n", all_file[idx], all_file[idx2]);
align_id(all_file[idx], all_file[idx2], id);
printf("%s\n", id);
break;
}
}
}
fclose(fp);
return 1;
}
int main(int argc, char *argv[])
{
static char *Spec[] = {"[-t]", NULL};
Process_Arguments(argc, argv, Spec, 1);
if (Is_Arg_Matched("-t")) {
/* Example test */
Stack *stack = Make_Stack(GREY, 7, 7, 1);
One_Stack(stack);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
/* set seeds */
Set_Stack_Pixel(ws->mask, 1, 1, 0, 0, 1.0);
Set_Stack_Pixel(ws->mask, 1, 5, 0, 0, 2.0);
Set_Stack_Pixel(ws->mask, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(ws->mask, 5, 1, 0, 0, 4.0);
Set_Stack_Pixel(ws->mask, 5, 5, 0, 0, 5.0);
/* set stack values */
Set_Stack_Pixel(stack, 1, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 1, 5, 0, 0, 3.0);
Set_Stack_Pixel(stack, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 5, 0, 0, 3.0);
Stack *out = Stack_Watershed(stack, ws);
//Write_Stack("../data/test/watershed/golden/watershed1.tif", out);
char *golden_file = "../data/test/watershed/golden/watershed1.tif";
if (fexist(golden_file)) {
Stack *golden = Read_Stack(golden_file);
if (Stack_Identical(out, golden) == FALSE) {
Print_Stack_Value(stack);
Print_Stack_Value(out);
Print_Stack_Value(golden);
PRINT_EXCEPTION("Bug?", "Conflict with golden.");
return 1;
}
Kill_Stack(stack);
Kill_Stack(out);
Kill_Stack(golden);
Kill_Stack_Watershed_Workspace(ws);
} else {
printf("%s cannot be found.\n", golden_file);
}
char *test_file = "../data/benchmark/rice_label.tif";
if (fexist(test_file)) {
stack = Read_Stack_U(test_file);
ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Copy_Stack(stack);
ws->conn = 26;
One_Stack(stack);
out = Stack_Watershed(stack, ws);
//Write_Stack("../data/test/watershed/golden/watershed2.tif", out);
Stack *golden = Read_Stack("../data/test/watershed/golden/watershed2.tif");
if (Stack_Identical(out, golden) == FALSE) {
PRINT_EXCEPTION("Bug?", "Conflict with golden.");
return 1;
}
} else {
printf("%s cannot be found.\n", test_file);
}
printf(":) Testing passed.\n");
return 0;
}
#if 0
/* Initialize */
Watershed_3d *watershed = New_Watershed_3d();
Watershed_3d_Workspace *ws = New_Watershed_3d_Workspace();
ws->conn = 26;
/* Initialize stack */
Stack *stack = Read_Stack("../data/fly_neuron/dist.tif");
int nvoxel = Stack_Voxel_Number(stack);
int i;
uint16 *array16 = (uint16 *)stack->array;
for (i = 0; i < nvoxel; i++) {
array16[i] = 0xFFFF - array16[i];
}
/* Add mask to ignore dark voxels */
ws->mask = Copy_Stack(stack);
//Translate_Stack(stack, GREY, 1);
//stack->array = stack->array + stack->width * stack->height * 100;
//stack->depth = 1;
// ws->mask = Copy_Stack(stack);
//Stack_Binarize(ws->mask);
// ws->mask = NULL;
//Write_Stack("../data/dist.tif", stack);
//Stack *stack2 = Copy_Stack(stack);
# if 0
Build_3D_Watershed(stack, watershed, ws);
Write_Stack("../data/test.tif", watershed->labels);
# endif
# if 0
Image_View iv = Image_View_Stack(stack2);
Watershed_Test *watershed2 = Build_2D_Watershed_Test(&(iv.image), 0);
Write_Image("../data/test2.tif", watershed2->labels);
# endif
#endif
#if 0
Image *image = Read_Image("../data/Ring15.tif_Sub1200_Original_inv.tif");
Watershed_2D *ws = Build_2D_Watershed(image, 0);
Image *result = Color_Watersheds(ws, image);
Write_Image("../data/test.tif", result);
Kill_Image(image);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 7, 7, 1);
One_Stack(stack);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
Set_Stack_Pixel(ws->mask, 1, 1, 0, 0, 1.0);
Set_Stack_Pixel(ws->mask, 1, 5, 0, 0, 2.0);
Set_Stack_Pixel(ws->mask, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(ws->mask, 5, 1, 0, 0, 4.0);
Set_Stack_Pixel(ws->mask, 5, 5, 0, 0, 5.0);
Set_Stack_Pixel(stack, 1, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 1, 5, 0, 0, 3.0);
Set_Stack_Pixel(stack, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 5, 0, 0, 3.0);
Stack *out = Stack_Watershed(stack, ws);
Print_Stack_Value(out);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 3, 3, 1);
One_Stack(stack);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
Set_Stack_Pixel(ws->mask, 0, 0, 0, 0, 1.0);
Set_Stack_Pixel(ws->mask, 2, 2, 0, 0, 2.0);
Set_Stack_Pixel(stack, 0, 0, 0, 0, 5.0);
Set_Stack_Pixel(stack, 2, 2, 0, 0, 3.0);
Set_Stack_Pixel(stack, 0, 2, 0, 0, 2.0);
//Set_Stack_Pixel(stack, 1, 1, 0, 0, 2.0);
Set_Stack_Pixel(stack, 1, 2, 0, 0, 2.0);
Set_Stack_Pixel(stack, 2, 0, 0, 0, 2.0);
Set_Stack_Pixel(stack, 2, 1, 0, 0, 2.0);
Print_Stack_Value(stack);
ws->start_level = 6;
Stack *out = Stack_Watershed(stack, ws);
Print_Stack_Value(out);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/benchmark/rice_label.tif");
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Copy_Stack(stack);
ws->conn = 26;
One_Stack(stack);
tic();
Stack *out = Stack_Watershed(stack, ws);
printf("%lld\n", toc());
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/diadem_d1_147.xml");
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
ws->conn = 26;
const int *dx = Stack_Neighbor_X_Offset(ws->conn);
const int *dy = Stack_Neighbor_X_Offset(ws->conn);
const int *dz = Stack_Neighbor_X_Offset(ws->conn);
int seed[3];
String_Workspace *sw = New_String_Workspace();
char *line = NULL;
FILE *fp = fopen("../data/diadem_d1_root_z.txt", "r");
int k = 1;
while ((line = Read_Line(fp, sw)) != NULL) {
int n;
String_To_Integer_Array(line, seed, &n);
double maxv = -1;
if (n == 3) {
maxv = Get_Stack_Pixel(stack, seed[0], seed[1], seed[2], 0);
printf("%g\n", maxv);
int i;
for (i = 0; i < ws->conn; i++) {
if (maxv < Get_Stack_Pixel(stack, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0)) {
maxv = Get_Stack_Pixel(stack, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0);
}
}
//Set_Stack_Pixel(stack, seed[0], seed[1], seed[2], 0, maxv);
Set_Stack_Pixel(ws->mask, seed[0], seed[1], seed[2], 0, k);
for (i = 0; i < ws->conn; i++) {
//Set_Stack_Pixel(stack, seed[0] + dx[i], seed[1] + dy[i],
// seed[2] + dz[i], 0, maxv);
Set_Stack_Pixel(ws->mask, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0, k);
}
k++;
}
}
fclose(fp);
Kill_String_Workspace(sw);
/*
Set_Stack_Pixel(ws->mask, 19, 605, 112, 0, 1.0);
Set_Stack_Pixel(ws->mask, 28, 565, 112, 0, 1.0);
*/
Stack_Watershed_Infer_Parameter(stack, ws);
tic();
Stack *out = Stack_Watershed(stack, ws);
printf("%lld\n", toc());
Write_Stack("../data/diadem_d1_147_label.tif", out);
static const uint8 Color_Map[][3] = {
{0, 0, 0},
{0, 224, 64}, {32, 64, 128}, {64, 64, 0}, {64, 128, 64},
{96, 64, 128}, {64, 0, 0}, {128, 200, 64}, {160, 128, 128},
{192, 0, 0}, {192, 160, 64}, {224, 64, 128}, {224, 224, 192}};
Translate_Stack(out, COLOR, 1);
size_t nvoxel = Stack_Voxel_Number(out);
size_t i;
color_t *arrayc = (color_t*) out->array;
for (i = 0; i < nvoxel; i++) {
arrayc[i][2] = Color_Map[arrayc[i][0]][2];
arrayc[i][1] = Color_Map[arrayc[i][0]][1];
arrayc[i][0] = Color_Map[arrayc[i][0]][0];
}
Write_Stack("../data/diadem_d1_147_paint.tif", out);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/diadem_d1_146.xml");
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
Stack *mask = Read_Stack("../data/test3.tif");
ws->mask = Crop_Stack(mask, 252, -937, 2, 1024, 1024, 63, NULL);
ws->conn = 26;
Stack_Watershed_Infer_Parameter(stack, ws);
tic();
Stack *out = Stack_Watershed(stack, ws);
printf("%lld\n", toc());
Write_Stack("../data/test2.tif", out);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 7, 7, 1);
One_Stack(stack);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
Set_Stack_Pixel(ws->mask, 1, 1, 0, 0, 1.0);
Set_Stack_Pixel(ws->mask, 1, 5, 0, 0, 2.0);
Set_Stack_Pixel(ws->mask, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(ws->mask, 5, 1, 0, 0, 4.0);
Set_Stack_Pixel(ws->mask, 5, 5, 0, 0, 5.0);
Set_Stack_Pixel(stack, 1, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 1, 5, 0, 0, 3.0);
Set_Stack_Pixel(stack, 3, 3, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 1, 0, 0, 3.0);
Set_Stack_Pixel(stack, 5, 5, 0, 0, 3.0);
Stack *out = Stack_Watershed(stack, ws);
Print_Stack_Value(out);
Stack *out2 = Stack_Region_Border_Shrink(out, ws);
Print_Stack_Value(out2);
#endif
#if 0
Stack *stack = Read_Stack("../data/diadem_d1_013_label.tif");
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
//ws->conn = 26;
Stack *out = Stack_Region_Border_Shrink(stack, ws);
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 1, 1, 19);
One_Stack(stack);
stack->array[3] = 5;
stack->array[4] = 5;
stack->array[7] = 5;
stack->array[8] = 5;
stack->array[10] = 4;
stack->array[11] = 5;
stack->array[12] = 5;
stack->array[13] = 4;
stack->array[16] = 5;
stack->array[17] = 5;
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
Print_Stack_Value(stack);
Stack_Watershed_Zgap_Barrier(stack, ws->mask);
Print_Stack_Value(ws->mask);
#endif
#if 0
Stack *stack = Read_Stack("../data/diadem_d1_047_label.tif");
Stack_Binarize(stack);
Stack *stack2 = Stack_Bwdist_L_U16(stack, NULL, 0);
Write_Stack("../data/test.tif", stack2);
#endif
#if 0
char stack_path[100];
char mask_path[100];
strcpy(stack_path, "../data/diadem_d1_064.xml");
strcpy(mask_path, stack_path);
strsplit(mask_path, '.', -1);
sprintf(mask_path, "%s_label.tif", mask_path);
if (!fexist(stack_path)) {
fprintf(stderr, "Cannot find %s\n", stack_path);
return 1;
}
printf("Processing %s\n", stack_path);
Stack *stack = Read_Stack_U(stack_path);
Stack *mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(mask);
int conn = 26;
const int *dx = Stack_Neighbor_X_Offset(conn);
const int *dy = Stack_Neighbor_X_Offset(conn);
const int *dz = Stack_Neighbor_X_Offset(conn);
int seed[3];
String_Workspace *sw = New_String_Workspace();
char *line = NULL;
FILE *fp = fopen("../data/064.seeds.txt", "r");
int k = 1;
/* label seeds */
while ((line = Read_Line(fp, sw)) != NULL) {
int n;
String_To_Integer_Array(line, seed, &n);
double maxv = -1;
if (n == 3) {
maxv = Get_Stack_Pixel(stack, seed[0], seed[1], seed[2], 0);
int i;
for (i = 0; i < conn; i++) {
if (maxv < Get_Stack_Pixel(stack, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0)) {
maxv = Get_Stack_Pixel(stack, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0);
}
}
Set_Stack_Pixel(mask, seed[0], seed[1], seed[2], 0, k);
for (i = 0; i < conn; i++) {
Set_Stack_Pixel(mask, seed[0] + dx[i], seed[1] + dy[i],
seed[2] + dz[i], 0, k);
}
k++;
}
}
fclose(fp);
Kill_String_Workspace(sw);
Stack_Running_Median(stack, 0, stack);
Stack_Running_Median(stack, 1, stack);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = mask;
Filter_3d *filter = Gaussian_Filter_3d(2.0, 2.0, 1.5);
Stack *filtered_stack = Filter_Stack(stack, filter);
Stack_Watershed_Zgap_Barrier(filtered_stack, ws->mask);
Stack_Running_Max(ws->mask, 0, ws->mask);
Stack_Running_Max(ws->mask, 1, ws->mask);
//Write_Stack("../data/test.tif", ws->mask);
Kill_Stack(filtered_stack);
filtered_stack = NULL;
FMatrix *dm = Mexihat_3D1_F(2.0, NULL, 2);
//FMatrix *dm = Mexihat_3D_F(2.0, NULL);
FMatrix_Negative(dm);
filtered_stack = Filter_Stack(stack, dm);
Stack_Threshold_Common(filtered_stack, 0, 65535);
Stack_Binarize(filtered_stack);
Translate_Stack(filtered_stack, GREY, 1);
{
int i, j, k;
int offset = 0;
uint16 *array = (uint16*) stack->array;
for (k = 0; k < stack->depth; k++) {
for (j = 0; j < stack->height; j++) {
for (i = 0; i < stack->width; i++) {
if (filtered_stack != NULL) {
if (filtered_stack->array[offset] == 1) {
ws->mask->array[offset] = STACK_WATERSHED_BARRIER;
}
}
array[offset++] += k * 2;
}
}
}
}
Kill_Stack(filtered_stack);
Stack_Watershed_Infer_Parameter(stack, ws);
ws->conn = 6;
double weights[26] = {0.5, 0.5, 1.0, 1.0, 0.2, 0.2, 0.75, 0.75, 0.75, 0.75,
0.35, 0.35, 0.35, 0.35, 0.6, 0.6, 0.6, 0.6,
0.45, 0.45, 0.45, 0.45,
0.45, 0.45, 0.45, 0.45};
ws->weights = weights;
ws->weights = NULL;
if (ws->weights != NULL) {
ws->min_level /= 3;
}
Stack_Running_Median(stack, 0, stack);
Stack_Running_Median(stack, 1, stack);
Stack *out = Stack_Watershed(stack, ws);
strcpy(mask_path, stack_path);
strsplit(mask_path, '.', -1);
sprintf(mask_path, "%s_label.tif", mask_path);
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack *stack = Read_Stack("../data/test/soma2.tif");
int thre = Stack_Find_Threshold_A(stack, THRESHOLD_LOCMAX_TRIANGLE);
Filter_3d *filter = Gaussian_Filter_3d(1.0, 1.0, 0.5);
Stack *out = Filter_Stack(stack, filter);
stack = Copy_Stack(out);
Stack_Threshold_Binarize(out, thre);
Stack *out2 = Stack_Bwdist_L_U16P(out, NULL, 0);
int nvoxel = Stack_Voxel_Number(out);
uint16_t *dist_array = (uint16_t*) out2->array;
int i;
for (i = 0; i < nvoxel; i++) {
dist_array[i] = sqrt(dist_array[i]);
}
Write_Stack("../data/labmeeting13/distp.tif", out2);
#endif
#if 0
//Stack *stack = Read_Stack("../data/test/soma2.tif");
Stack *stack = Read_Stack("/Users/zhaot/Data/jinny/slice7_2to34ds_soma_c2.tif");
int thre = Stack_Find_Threshold_A(stack, THRESHOLD_LOCMAX_TRIANGLE);
Filter_3d *filter = Gaussian_Filter_3d(1.0, 1.0, 0.5);
Stack *out = Filter_Stack(stack, filter);
stack = Copy_Stack(out);
Stack_Threshold_Binarize(out, thre);
Stack *out2 = Stack_Bwdist_L_U16P(out, NULL, 0);
/*
out = Stack_Locmax_Region(out2, 26);
*/
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(ws->mask);
size_t nvoxel = Stack_Voxel_Number(stack);
size_t offset;
uint16_t *dist_array = (uint16_t*) out2->array;
for (offset = 0; offset < nvoxel; offset++) {
if (/*(out->array[offset] == 1) && */(dist_array[offset] > 1000)) {
ws->mask->array[offset] = 1;
}
}
//Objlabel_Workspace *ow = New_Objlabel_Workspace();
//Stack_Label_Large_Objects_W(ws->mask, 1, 2, 10, ow);
//Stack_Label_Objects_N(ws->mask, NULL, 1, 2, 26);
Object_3d_List *objs = Stack_Find_Object(ws->mask, 1, 100);
Zero_Stack(ws->mask);
Stack_Draw_Objects_Bw(ws->mask, objs, -255);
printf("%g\n", Stack_Max(ws->mask, NULL));
/*
Write_Stack("../data/test.tif", ws->mask);
return 1;
*/
ws->min_level = thre;
ws->start_level = 65535;
Stack *out3 = Stack_Watershed(stack, ws);
/*
Write_Stack("../data/labmeeting13/watershed.tif", out3);
return 1;
*/
for (offset = 0; offset < nvoxel; offset++) {
if (dist_array[offset] < 300) {
out3->array[offset] = 0;
}
}
int nregion = Stack_Max(out3, NULL);
Kill_Stack(out2);
Stack *filtered = Copy_Stack(stack);
Kill_Stack(stack);
ws->conn = 8;
stack = Stack_Region_Border_Shrink(out3, ws);
out2 = Stack_Region_Expand(stack, 4, 30, NULL);
for (offset = 0; offset < nvoxel; offset++) {
if (out->array[offset] == 0) {
out2->array[offset] = 0;
}
}
Write_Stack("../data/test2.tif", out2);
Kill_Stack(stack);
//stack = Read_Stack("../data/test/soma2.tif");
stack = Read_Stack("/Users/zhaot/Data/jinny/slice7_2to34ds_soma_c2.tif");
Translate_Stack(stack, COLOR, 1);
int i;
double h = 0.0;
double s = 1.0;
for (i = 0; i < nregion; i++) {
Stack_Label_Color_L(stack, out2, i+1, h+=0.35, s, filtered);
/*
Rgb_Color color;
Set_Color_Jet(&color, i*3);
Stack_Label_Level(stack, out2, i+1, color);
*/
}
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Stack *stack = Read_Stack("../data/leaktest/leak3.tif");
Stack *distmap = Stack_Bwdist_L_U16P(stack, NULL, 0);
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->mask = Copy_Stack(distmap);
Stack_Threshold_Binarize(ws->mask, 10);
Translate_Stack(ws->mask, GREY, 1);
Object_3d_List *objs = Stack_Find_Object(ws->mask, 1, 100);
Zero_Stack(ws->mask);
Stack_Draw_Objects_Bw(ws->mask, objs, -255);
ws->min_level = 1;
ws->start_level = 65535;
Stack *out3 = Stack_Watershed(distmap, ws);
Write_Stack("../data/test.tif", out3);
#endif
#if 0
Stack *stack = Read_Stack("../data/benchmark/two_disk.tif");
Stack_Watershed_Workspace *ws = Make_Stack_Watershed_Workspace(stack);
ws->conn = 26;
Stack *out = Stack_Watershed(stack, ws);
Write_Stack("../data/test.tif", out);
#endif
return 0;
}
int main(int argc, char *argv[])
{
static char *Spec[] = {"[-t]", NULL};
Process_Arguments(argc, argv, Spec, 1);
if (Is_Arg_Matched("-t")) {
coordinate_3d_t coord = {0, 0, 0};
/* Translate coordinates. */
Geo3d_Translate_Coordinate(coord, coord+1, coord+2, 1.0, 2.0, 3.0);
if ((coord[0] != 1.0) || (coord[1] != 2.0) || (coord[2] != 3.0)) {
Print_Coordinate_3d(coord);
PRINT_EXCEPTION(":( Bug?", "Unexpected coordinate values.");
return 1;
}
coordinate_3d_t coord2 = {0, 0, 0};
double dx, dy, dz;
Geo3d_Coordinate_Offset(coord[0], coord[1], coord[2], coord2[0], coord2[1],
coord2[2], &dx, &dy, &dz);
if ((dx != -coord[0]) || (dy != -coord[1]) || (dz != -coord[2])) {
PRINT_EXCEPTION(":( Bug?", "Unexpected offset values.");
return 1;
}
Coordinate_3d_Copy(coord2, coord);
/* Rotate coordinates. */
Geo3d_Rotate_Coordinate(coord, coord+1, coord+2, 0.1, 0.5, 0);
if (fabs(Geo3d_Orgdist_Sqr(coord[0], coord[1], coord[2]) -
Geo3d_Orgdist_Sqr(coord2[0], coord2[1], coord2[2])) > 0.01) {
PRINT_EXCEPTION(":( Bug?", "Rotation failed.");
return 1;
}
/* inverse rotation */
Geo3d_Rotate_Coordinate(coord, coord+1, coord+2, 0.1, 0.5, 1);
if ((fabs(coord[0] - coord2[0]) > 0.01) ||
(fabs(coord[1] - coord2[1]) > 0.01) ||
(fabs(coord[2] - coord2[2]) > 0.01)){
PRINT_EXCEPTION(":( Bug?", "Rotation failed.");
return 1;
}
/* Normal vector of an orientation. This is a canonical representaion
* of an orientation. */
Geo3d_Orientation_Normal(0.1, 0.5, coord, coord+1, coord+2);
/* We can also turn the normal vector into orientation. */
double theta, psi;
Geo3d_Normal_Orientation(coord[0], coord[1], coord[2], &theta, &psi);
if (fabs(theta - 0.1) > 0.01 || fabs(Normalize_Radian(psi) - 0.5) > 0.01) {
printf("%g, %g\n", theta, psi);
PRINT_EXCEPTION(":( Bug?", "Unexpected orientation values.");
return 1;
}
/* If we rotate the vector back, we should get (0, 0, 1). */
Geo3d_Rotate_Coordinate(coord, coord+1, coord+2, 0.1, 0.5, 1);
if ((fabs(coord[0]) > 0.01) || (fabs(coord[1]) > 0.01) ||
(fabs(coord[2] - 1.0) > 0.01)){
PRINT_EXCEPTION(":( Bug?", "Rotation failed.");
return 1;
}
Geo3d_Coord_Orientation(1, 0, 0, &theta, &psi);
double in[3] = {0, 0, 1};
double out[3] = {0, 0, 0};
Rotate_XZ(in, out, 1, theta, psi, 0);
if (fabs(out[0] - 1.0) > 0.01 || fabs(out[1]) > 0.01 ||
fabs(out[2]) > 0.01) {
printf("%g, %g, %g\n", out[0], out[1], out[2]);
printf("%g, %g\n", theta, psi);
PRINT_EXCEPTION(":( Bug?", "Unexpected orientation values.");
return 1;
}
/*
if (fabs(theta - TZ_PI_2) > 0.01 ||
fabs(Normalize_Radian(psi) - TZ_PI_2) > 0.01) {
printf("%g, %g\n", theta, psi);
PRINT_EXCEPTION(":( Bug?", "Unexpected orientation values.");
return 1;
}
*/
Geo3d_Coord_Orientation(5, 0, 0, &theta, &psi);
{
double in[3] = {0, 0, 5};
double out[3] = {0, 0, 0};
Rotate_XZ(in, out, 1, theta, psi, 0);
if (fabs(out[0] - 5.0) > 0.01 || fabs(out[1]) > 0.01 ||
fabs(out[2]) > 0.01) {
printf("%g, %g, %g\n", out[0], out[1], out[2]);
printf("%g, %g\n", theta, psi);
PRINT_EXCEPTION(":( Bug?", "Unexpected orientation values.");
return 1;
}
}
/*
if (fabs(theta - TZ_PI_2) > 0.01 ||
fabs(Normalize_Radian(psi) - TZ_PI_2) > 0.01) {
printf("%g, %g\n", theta, psi);
PRINT_EXCEPTION(":( Bug?", "Unexpected orientation values.");
return 1;
}
*/
/* Rotate the orientation. */
theta = TZ_PI_2;
psi = TZ_PI;
Geo3d_Rotate_Orientation(-TZ_PI, TZ_PI_2, &theta, &psi);
if (fabs(theta + TZ_PI_2) > 0.01 ||
fabs(psi + TZ_PI_2) > 0.01) {
printf("%g, %g\n", theta, psi);
PRINT_EXCEPTION(":( Bug?", "Unexpected orientation values.");
return 1;
}
/* More extensive test on rotation */
Random_Seed(time(NULL) - getpid());
int i;
for (i = 0; i < 100; i++) {
double x = Unifrnd() * (1 - Bernrnd(0.5) * 2.0);
double y = Unifrnd() * (1 - Bernrnd(0.5) * 2.0);
double z = Unifrnd() * (1 - Bernrnd(0.5) * 2.0);
double theta, psi;
Geo3d_Coord_Orientation(x, y, z, &theta, &psi);
double x2 = 0.0;
double y2 = 0.0;
double z2 = Geo3d_Orgdist(x, y, z);
Geo3d_Rotate_Coordinate(&x2, &y2, &z2, theta, psi, 0);
if (fabs(x - x2) > 0.01 || fabs(y - y2) > 0.01 || fabs(z - z2) > 0.01) {
printf("%g, %g\n", theta, psi);
printf("%g, %g, %g\n", x, y, z);
printf("%g, %g, %g\n", x2, y2, z2);
PRINT_EXCEPTION(":( Bug?", "Unexpected orientation values.");
return 1;
}
}
/* Dot product. */
if (Geo3d_Dot_Product(1.0, 2.0, 3.0, 3.0, 2.0, 1.0) != 10.0) {
PRINT_EXCEPTION(":( Bug?", "Unexpected dot product.");
return 1;
}
/* Cross product. */
Geo3d_Cross_Product(1.0, 2.0, 3.0, 3.0, 1.0, 2.0, coord, coord+1, coord+2);
if (fabs(Geo3d_Dot_Product(1.0, 2.0, 3.0, coord[0], coord[1], coord[2])) >
0.01) {
PRINT_EXCEPTION(":( Bug?", "Unexpected dot product.");
return 1;
}
if (fabs(Geo3d_Dot_Product(3.0, 1.0, 2.0, coord[0], coord[1], coord[2])) >
0.01) {
PRINT_EXCEPTION(":( Bug?", "Unexpected dot product.");
return 1;
}
/* Distance calculations. */
if (Geo3d_Orgdist_Sqr(1.0, 2.0, 3.0) != 14.0) {
PRINT_EXCEPTION(":( Bug?", "Unexpected value.");
return 1;
}
if (fabs(Geo3d_Orgdist(1.0, 2.0, 3.0) - sqrt(14.0)) > 0.01) {
PRINT_EXCEPTION(":( Bug?", "Unexpected value.");
return 1;
}
if (Geo3d_Dist(1.0, 2.0, 3.0, 1.0, 2.0, 3.0) != 0.0) {
PRINT_EXCEPTION(":( Bug?", "Unexpected value.");
return 1;
}
if (Geo3d_Dist_Sqr(1.0, 2.0, 3.0, 0.0, 0.0, 0.0) != 14.0) {
PRINT_EXCEPTION(":( Bug?", "Unexpected value.");
return 1;
}
/* Angle between two vectors. */
if (fabs(Geo3d_Angle2(1, 0, 0, 0, 0, 1) - TZ_PI_2) > 0.01) {
PRINT_EXCEPTION(":( Bug?", "Unexpected value.");
return 1;
}
/* Distance between two lines */
coordinate_3d_t line1_start = {0, 0, 0};
coordinate_3d_t line1_end = {1, 0, 0};
coordinate_3d_t line2_start = {0, 1, 1};
coordinate_3d_t line2_end = {0, 2, 1};
double d = Geo3d_Line_Line_Dist(line1_start, line1_end,
line2_start, line2_end);
if (fabs(d - 1.0) > 0.01) {
PRINT_EXCEPTION(":( Bug?", "Unexpected distance.");
return 1;
}
/* Distance between two line segments. */
double intersect1, intersect2;
int cond;
d = Geo3d_Lineseg_Lineseg_Dist(line1_start, line1_end,
line2_start, line2_end,
&intersect1, &intersect2, &cond);
if (fabs(d - sqrt(2.0)) > 0.01) {
PRINT_EXCEPTION(":( Bug?", "Unexpected distance.");
return 1;
}
/* Distance between a point and a line segment. */
coord[0] = 0.5;
coord[1] = 1.0;
coord[2] = 1.0;
d = Geo3d_Point_Lineseg_Dist(coord, line1_start, line1_end, &intersect1);
if (fabs(d - sqrt(2.0)) > 0.01) {
PRINT_EXCEPTION(":( Bug?", "Unexpected distance.");
return 1;
}
/* Get a break point of a line segment. */
Geo3d_Lineseg_Break(line1_start, line1_end, 0.1, coord);
if ((coord[0] != 0.1) || (coord[1] != 0.0) || (coord[2] != 0.0)) {
PRINT_EXCEPTION(":( Bug?", "Unexpected break point.");
return 1;
}
/* Orientations of a set of points */
/* Orientation of a covariance matrix */
/* 3D coordinates routines */
/* Unitize a point. */
Coordinate_3d_Unitize(coord);
if (fabs(Coordinate_3d_Norm(coord) - 1.0) > 0.01) {
PRINT_EXCEPTION(":( Bug?", "Unexpected norm.");
return 1;
}
Set_Coordinate_3d(coord, 0.0, 0.0, 0.0);
/* origin point is not affected by unitization */
Coordinate_3d_Unitize(coord);
if (Coordinate_3d_Norm(coord) != 0.0) {
PRINT_EXCEPTION(":( Bug?", "Unexpected norm.");
return 1;
}
Set_Coordinate_3d(coord, 1.0, 2.0, 3.0);
/* Square length */
if (Coordinate_3d_Length_Square(coord) != 14) {
PRINT_EXCEPTION(":( Bug?", "Unexpected square length");
}
/* Angle between two vectors */
coordinate_3d_t coord_a1 = { 1, 0, 0 };
coordinate_3d_t coord_a2 = { 0, 0, 1 };
if (fabs(Coordinate_3d_Angle2(coord_a1, coord_a2) - TZ_PI_2) > 0.01) {
PRINT_EXCEPTION(":( Bug?", "Unexpected angle");
}
/* Scale coordinates */
Coordinate_3d_Scale(coord, 2.0);
if ((coord[0] != 2.0) || (coord[1] != 4.0) || (coord[2] != 6.0)) {
PRINT_EXCEPTION(":( Bug?", "Unexpected coordinate value.");
return 1;
}
/* Normalizd dot product */
if (Coordinate_3d_Normalized_Dot(coord, coord2) > 1.0) {
PRINT_EXCEPTION(":( Bug?", "Unexpected dot product.");
return 1;
}
Set_Coordinate_3d(coord, 1.0, 2.0, 3.0);
Coordinate_3d_Copy(coord2, coord);
Coordinate_3d_Scale(coord2, 2.0);
coordinate_3d_t coord3;
Coordinate_3d_Copy(coord3, coord);
Coordinate_3d_Scale(coord3, 3.0);
/* cos value of an angle formed by 3 points */
if (Coordinate_3d_Cos3(coord, coord2, coord3) != 1.0) {
PRINT_EXCEPTION(":( Bug?", "Unexpected cos value.");
return 1;
}
/* cos value of an angle formed by 4 points */
coordinate_3d_t coord4;
Coordinate_3d_Copy(coord4, coord);
Coordinate_3d_Scale(coord4, 4.0);
if (Coordinate_3d_Cos4(coord, coord2, coord3, coord4) != 1.0) {
PRINT_EXCEPTION(":( Bug?", "Unexpected cos value.");
return 1;
}
printf(":) Testing passed.\n");
return 0;
}
#if 0
Geo3d_Vector v1 = {1.1, 0, 0};
Geo3d_Vector v2 = {5, 0, 0};
double theta1 = 3.83812;
double psi1 = 3.53202;
double theta2 = 0.72657;
double psi2 = 3.61214;
Geo3d_Orientation_Normal(theta1, psi1, &(v1.x), &(v1.y), &(v1.z));
Geo3d_Orientation_Normal(theta2, psi2, &(v2.x), &(v2.y), &(v2.z));
Print_Geo3d_Vector(&v1);
Print_Geo3d_Vector(&v2);
printf("%g\n", Geo3d_Vector_Dot(&v1, &v2));
printf("%g\n", Geo3d_Vector_Angle2(&v1, &v2));
double angle = Vector_Angle(-1.0, -1.0);
theta1 = -3.0;
psi1 = -5.0;
double x, y, z;
Geo3d_Orientation_Normal(theta1, psi1, &x, &y, &z);
printf("%g, %g, %g\n", x, y, z);
Geo3d_Normal_Orientation(x, y, z, &theta1, &psi1);
printf("%g\n", angle * 180.0 / TZ_PI);
printf("%g, %g\n", theta1, psi1);
Geo3d_Orientation_Normal(theta1, psi1, &x, &y, &z);
printf("%g, %g, %g\n", x, y, z);
#endif
#if 0
Geo3d_Scalar_Field *field =
Read_Geo3d_Scalar_Field("../data/mouse_neuron/seeds.bn");
Print_Geo3d_Scalar_Field_Info(field);
Stack *stack = Read_Stack("../data/mouse_neuron/mask.tif");
Geo3d_Scalar_Field_Draw_Stack(field, stack, NULL, NULL);
Write_Stack("../data/test.tif", stack);
#endif
#if 0
double line_start[3] = {2.0, 3.0, 4.0};
double line_end[3] = {1.0, 1.0, 6.0};
double point[3] = {10.5, 20.5, 40.7};
double lamda;
printf("%g\n", Geo3d_Point_Lineseg_Dist(point, line_start, line_end, &lamda));
double line_point[3];
double length = sqrt(Geo3d_Dist_Sqr(line_start[0], line_start[1], line_start[2], line_end[0], line_end[1], line_end[2]));
line_point[0] = line_start[0] + lamda * (line_end[0] - line_start[0]);
line_point[1] = line_start[1] + lamda * (line_end[1] - line_start[1]);
line_point[2] = line_start[2] + lamda * (line_end[2] - line_start[2]);
printf("%g\n", lamda);
printf("%g\n", sqrt(Geo3d_Dist_Sqr(line_point[0], line_point[1], line_point[2], point[0], point[1], point[2])));
darray_sub(point, line_point, 3);
darray_sub(line_end, line_point, 3);
printf("%g\n", Geo3d_Dot_Product(point[0], point[1], point[2],
line_end[0], line_end[1], line_end[2]));
#endif
#if 0
Geo3d_Scalar_Field *field = Read_Geo3d_Scalar_Field("../data/mouse_neuron3_org/seeds");
//Print_Geo3d_Scalar_Field(field);
darray_write("../data/pts.bn", (double *)field->points, field->size * 3);
darray_write("../data/ws.bn", field->values, field->size);
coordinate_3d_t centroid;
Geo3d_Scalar_Field_Centroid(field, centroid);
Print_Coordinate_3d(centroid);
double cov[9];
Geo3d_Scalar_Field_Cov(field, cov);
darray_print2(cov, 3, 3);
darray_write("../data/cov.bn", cov, 9);
double vec[3];
Geo3d_Cov_Orientation(cov, vec);
darray_print2(vec, 3, 1);
#endif
#if 0
double mu1, mu2;
# if 0 /* parallel case */
double line1_start[3] = {0, 0, 0};
double line1_end[3] = {1, 1, 10};
double line2_start[3] = {0, 1, 0};
double line2_end[3] = {1, 2, 10};
# endif
# if 0 /* parallel case */
double line1_start[3] = {0, 0, 0};
double line1_end[3] = {1, 1, 10};
double line2_start[3] = {-1, -1, -1};
double line2_end[3] = {-3, -3, -21};
# endif
# if 0 /* i-i case */
double line1_start[3] = {0, 0, 0};
double line1_end[3] = {3, 4, 5};
double line2_start[3] = {-1, 8, 9};
double line2_end[3] = {1, -3, -4};
# endif
# if 0 /* point to line case */
double line1_start[3] = {3, 4, 5};
double line1_end[3] = {3, 4, 5};
double line2_start[3] = {-1, 8, 9};
double line2_end[3] = {1, -3, -4};
# endif
# if 0 /* point to line case */
double line2_start[3] = {3, 4, 5};
double line2_end[3] = {3, 4, 5};
double line1_start[3] = {-1, 8, 9};
double line1_end[3] = {1, -3, -4};
# endif
# if 0 /* point to line case */
double line2_start[3] = {3, 4, 5};
double line2_end[3] = {3, 4, 5};
double line1_start[3] = {-1, 8, 9};
double line1_end[3] = {-1, 8, 9};
# endif
# if 0
double line1_start[3] = {256.062, 328.674, 67.9029};
double line1_end[3] = {246.162, 330.078, 67.9896};
double line2_start[3] = {262.368, 336.609, 68.3076};
double line2_end[3] = {259.956, 326.944, 67.4325};
# endif
int cond;
double dist = Geo3d_Lineseg_Lineseg_Dist(line1_start, line1_end,
line2_start, line2_end,
&mu1, &mu2, &cond);
printf("%d, %g\n", cond, dist);
dist = Geo3d_Line_Line_Dist(line1_start, line1_end, line2_start, line2_end);
printf("%g\n", dist);
#endif
#if 1
double *d = Unifrnd_Double_Array(12000000, NULL);
double *d2 = Unifrnd_Double_Array(12000000, NULL);
tic();
Rotate_XZ(d, d, 4000000, 0.1, 0.2, 1);
printf("%llu\n", toc());
tic();
Rotate_XZ2(d, d, 4000000, 0.1, 0.2, 0);
printf("%llu\n", toc());
#endif
#if 0
double d[3] = {0.1, 0.2, 0.3};
Rotate_XZ(d, d, 1, 0.1, 0.2, 0);
darray_print2(d, 3, 1);
#endif
#if 0
printf("%g\n", Ellipse_Point_Distance(5, 5, 3, 5));
#endif
#if 0
Geo3d_Ellipse *ellipse = New_Geo3d_Ellipse();
ellipse->scale = 0.5;
ellipse->orientation[0] = 1.0;
Print_Geo3d_Ellipse(ellipse);
FILE *fp = fopen("../data/test.swc", "w");
Swc_Node node;
Geo3d_Ellipse_To_Swc_Node(ellipse, 1, -1, 1.0, 2, &node);
Swc_Node_Fprint(fp, &node);
/*
double pt[3] = {0.0, 0.0, 1.0};
printf("%g\n", Geo3d_Ellipse_Point_Distance(ellipse, pt));
*/
Geo3d_Ellipse *ellipse2 = Copy_Geo3d_Ellipse(ellipse);
ellipse2->center[0] += 10.0;
ellipse2->orientation[0] = 2.0;
ellipse2->radius += 3.0;
Geo3d_Ellipse *ellipse3 = Geo3d_Ellipse_Interpolate(ellipse, ellipse2, 0.2,
NULL);
Geo3d_Ellipse_To_Swc_Node(ellipse3, 2, 1, 1.0, 2, &node);
Swc_Node_Fprint(fp, &node);
Geo3d_Ellipse_To_Swc_Node(ellipse2, 3, 2, 1.0, 2, &node);
Swc_Node_Fprint(fp, &node);
Print_Geo3d_Ellipse(ellipse3);
fclose(fp);
#endif
#if 0
Geo3d_Ellipse *ellipse = New_Geo3d_Ellipse();
ellipse->scale = 0.5;
FILE *fp = fopen("../data/test.swc", "w");
coordinate_3d_t *pts = Geo3d_Ellipse_Sampling(ellipse, 20, 0, NULL);
Geo3d_Point_Array_Swc_Fprint(fp, pts, 20, 1, -1, 1.0, 2);
ellipse->orientation[0] = 1.0;
pts = Geo3d_Ellipse_Sampling(ellipse, 20, 0, NULL);
Geo3d_Point_Array_Swc_Fprint(fp, pts, 20, 21, -1, 1.0, 3);
ellipse->center[2] = 5.0;
pts = Geo3d_Ellipse_Sampling(ellipse, 20, 0, NULL);
Geo3d_Point_Array_Swc_Fprint(fp, pts, 20, 41, -1, 1.0, 4);
coordinate_3d_t vec[2];
Coordinate_3d_Copy(vec[0], ellipse->center);
Geo3d_Ellipse_First_Vector(ellipse, vec[1]);
Coordinate_3d_Add(vec[0], vec[1], vec[1]);
Geo3d_Point_Array_Swc_Fprint(fp, vec, 2, 101, -1, 1.0, 5);
Geo3d_Ellipse_Second_Vector(ellipse, vec[1]);
Coordinate_3d_Add(vec[0], vec[1], vec[1]);
Geo3d_Point_Array_Swc_Fprint(fp, vec, 2, 111, -1, 1.0, 6);
Geo3d_Ellipse_Normal_Vector(ellipse, vec[1]);
Coordinate_3d_Add(vec[0], vec[1], vec[1]);
Geo3d_Point_Array_Swc_Fprint(fp, vec, 2, 121, -1, 1.0, 7);
fclose(fp);
#endif
#if 0
Geo3d_Ellipse ep_array[10];
Geo3d_Ellipse *ellipse = New_Geo3d_Ellipse();
ellipse->scale = 0.5;
Geo3d_Ellipse_Copy(ep_array, ellipse);
FILE *fp = fopen("../data/test.swc", "w");
ellipse->orientation[0] += 0.5;
ellipse->center[2] += 3.0;
ellipse->center[0] += 1.0;
Geo3d_Ellipse_Copy(ep_array + 1, ellipse);
ellipse->center[2] += 3.0;
Geo3d_Ellipse_Copy(ep_array + 2, ellipse);
coordinate_3d_t *pts = Geo3d_Ellipse_Array_Sampling(ep_array, 3, 20, NULL);
Geo3d_Point_Array_Swc_Fprint(fp, pts, 60, 1, -1, 1.0, 2);
fclose(fp);
#endif
#if 0
printf("%g\n", Vector_Angle(1.0, 1.0) * 180 / TZ_PI);
#endif
#if 0
double theta, psi;
coordinate_3d_t coord;
coord[0] = 0.0822;
coord[1] = 0.1515;
coord[2] = 0.1369;
Geo3d_Coord_Orientation(coord[0], coord[1], coord[2], &theta, &psi);
printf("%g, %g\n", theta, psi);
Geo3d_Orientation_Normal(theta, psi, coord, coord+1, coord+2);
Print_Coordinate_3d(coord);
#endif
#if 0
double theta, psi;
double x = -1;
double y = 1.83697019872103e-16;
double z = 3;
Geo3d_Coord_Orientation(x, y, z, &theta, &psi);
#endif
#if 0
double theta = Vector_Angle2(0, 1, 1, 0, TRUE);
printf("angle: %g\n", theta);
theta = Vector_Angle2(0, 1, -1, 0, FALSE);
printf("angle: %g\n", theta);
theta = Vector_Angle2(-1, 0, -1, -1, TRUE);
printf("angle: %g\n", theta);
#endif
return 0;
}
/*
* trace_neuron - trace neuron from given seeds
*
* trace_neuron [!wtr] seed_file -Dsave_dir
* -r: write intermediate results
*
*/
int main(int argc, char* argv[])
{
static char *Spec[] = {
"[!wtr] [-canvas <string>] [-mask <string>] [-res <string>] [-minr <int>]",
"-minlen <double>",
" <image:string> -S<string> -D<string>",
NULL};
Process_Arguments(argc, argv, Spec, 1);
char *dir = Get_String_Arg("-D");
char file_path[100];
sprintf(file_path, "%s/%s", dir, Get_String_Arg("-S"));
printf("%s\n", file_path);
Geo3d_Scalar_Field *seed = Read_Geo3d_Scalar_Field(file_path);
int idx;
sprintf(file_path, "%s/%s.bn", dir, "max_r");
double max_r;
int tmp;
if (fexist(file_path)) {
darray_read2(file_path, &max_r, &tmp);
} else {
max_r = darray_max(seed->values, seed->size, &idx);
}
printf("%g\n", max_r);
max_r *= 1.5;
/*
sprintf(file_path, "%s/%s", dir, "soma0.bn");
if (!fexist(file_path)) {
max_r *= 2.0;
}
*/
Set_Neuroseg_Max_Radius(max_r);
Stack *signal = Read_Stack(Get_String_Arg("image"));
dim_type dim[3];
dim[0] = signal->width;
dim[1] = signal->height;
dim[2] = signal->depth;
/*
IMatrix *chord = Make_IMatrix(dim, 3);
Stack *code = Make_Stack(GREY16,
signal->width, signal->height, signal->depth);
*/
Rgb_Color color;
Set_Color(&color, 255, 0, 0);
Stack *canvas = NULL;
char trace_file_path[100];
sprintf(trace_file_path, "%s/%s", dir, Get_String_Arg("-canvas"));
if (fexist(trace_file_path) == 1) {
canvas = Read_Stack((char *) trace_file_path);
} else {
canvas = Copy_Stack(signal);
Stretch_Stack_Value_Q(canvas, 0.999);
Translate_Stack(canvas, COLOR, 1);
}
Stack *traced = NULL;
char trace_mask_path[100];
sprintf(trace_mask_path, "%s/%s", dir, Get_String_Arg("-mask"));
if (fexist(trace_mask_path) == 1) {
traced = Read_Stack((char *) trace_mask_path);
} else {
traced = Make_Stack(GREY, signal->width, signal->height, signal->depth);
One_Stack(traced);
}
//Object_3d *obj = NULL;
int seed_offset = -1;
Neurochain *chain = NULL;
double z_scale = 1.0;
if (Is_Arg_Matched("-res")) {
sprintf(file_path, "%s", Get_String_Arg("-res"));
if (fexist(file_path)) {
double res[3];
int length;
darray_read2(file_path, res, &length);
if (res[0] != res[1]) {
perror("Different X-Y resolutions.");
TZ_ERROR(ERROR_DATA_VALUE);
}
z_scale = res[0] / res[2];
}
}
//sprintf(file_path, "%s/%s", dir, Get_String_Arg("-M"));
//Stack *stack = Read_Stack(file_path);
tic();
FILE *fp = NULL;
char chain_file_path[100];
char vrml_file_path[100];
double min_chain_length = 25.0;
if (Is_Arg_Matched("-minlen")) {
min_chain_length = Get_Double_Arg("-minlen");
}
int *indices = iarray_malloc(seed->size);
double *values = darray_malloc(seed->size);
int i;
Local_Neuroseg *locseg = (Local_Neuroseg *)
malloc(seed->size * sizeof(Local_Neuroseg));
int index = 0;
for (i = 0; i < seed->size; i++) {
printf("-----------------------------> seed: %d / %d\n", i, seed->size);
indices[i] = i;
index = i;
int x = (int) seed->points[index][0];
int y = (int) seed->points[index][1];
int z = (int) seed->points[index][2];
double width = seed->values[index];
chain = New_Neurochain();
seed_offset = Stack_Util_Offset(x, y, z, signal->width, signal->height,
signal->depth);
if (width < 3.0) {
width += 0.5;
}
Set_Neuroseg(&(locseg[i].seg), width, width, 12.0,
0.0, 0.0, 0.0);
double cpos[3];
cpos[0] = x;
cpos[1] = y;
cpos[2] = z;
cpos[2] *= z_scale;
Set_Neuroseg_Position(&(locseg[i]), cpos, NEUROSEG_CENTER);
Stack_Fit_Score fs;
fs.n = 1;
fs.options[0] = 1;
values[i] = Local_Neuroseg_Orientation_Search_C(&(locseg[i]), signal, z_scale, &fs);
}
darray_qsort(values, indices, seed->size);
/*
for (i = 0; i < seed->size; i++) {
indices[i] = i;
}
darraycpy(values, seed->values, 0, seed->size);
darray_qsort(values, indices, seed->size);
*/
int counter = 0;
// for (i = seed->size - 1; i >= seed->size - 231; i--) {
for (i = seed->size - 1; i >= 0; i--) {
index = indices[i];
printf("-----------------------------> seed: %d / %d\n", i, seed->size);
sprintf(chain_file_path, "%s/chain%d.bn", dir, index);
sprintf(vrml_file_path, "%s/chain%d.wrl", dir, index);
if (fexist(chain_file_path) == 1) {
chain = Read_Neurochain(chain_file_path);
if (Neurochain_Geolen(chain) >= min_chain_length) {
Write_Neurochain_Vrml(vrml_file_path, chain);
Neurochain_Label(canvas, chain, z_scale);
Neurochain_Erase_E(traced, chain, z_scale, 0,
Neurochain_Length(chain, FORWARD),
1.5, 0.0);
}
Free_Neurochain(chain);
printf("chain exists\n");
continue;
}
int x = (int) seed->points[index][0];
int y = (int) seed->points[index][1];
int z = (int) seed->points[index][2];
if (*STACK_PIXEL_8(traced, x, y, z, 0) == 0) {
printf("traced \n");
continue;
}
double width = seed->values[index];
if (width > max_r) {
printf("too thick\n");
continue;
}
if (Is_Arg_Matched("-minr")) {
int max_level = (int) (width + 0.5);
if (max_level <= Get_Int_Arg("-minr")) {
printf("too thin\n");
continue;
}
}
/*
seed_offset = Stack_Util_Offset(x, y, z, signal->width, signal->height,
signal->depth);
*/
chain = New_Neurochain();
/*
Stack_Level_Code_Constraint(stack, code, chord->array, &seed_offset, 1,
max_level + 1);
Voxel_t v;
v[0] = x;
v[1] = y;
v[2] = z;
Stack *tmp_stack = Copy_Stack(stack);
obj = Stack_Grow_Object_Constraint(tmp_stack, 1, v, chord, code,
max_level);
Free_Stack(tmp_stack);
Print_Object_3d_Info(obj);
double vec[3];
Object_3d_Orientation_Zscale(obj, vec, MAJOR_AXIS, z_scale);
double theta, psi;
Geo3d_Vector obj_vec;
Set_Geo3d_Vector(&obj_vec, vec[0], vec[1], vec[2]);
Geo3d_Vector_Orientation(&obj_vec, &theta, &psi);
*/
/*
if (width < 3.0) {
width += 0.5;
}
Set_Neuroseg(&(chain->locseg.seg), width, width, 12.0,
0.0, 0.0, 0.0);
double cpos[3];
cpos[0] = x;
cpos[1] = y;
cpos[2] = z;
cpos[2] *= z_scale;
//Set_Neuroseg_Position(&(chain->locseg), cpos, NEUROSEG_BOTTOM);
Set_Neuroseg_Position(&(chain->locseg), cpos, NEUROSEG_CENTER);
Stack_Fit_Score fs;
fs.n = 1;
fs.options[0] = 1;
Local_Neuroseg_Orientation_Search_C(&(chain->locseg), signal, z_scale,
&fs);
//fs.options[0] = 1;
*/
Copy_Local_Neuroseg(&(chain->locseg), &(locseg[index]));
Neurochain *chain_head = chain;
if (Initialize_Tracing(signal, chain, NULL, z_scale) >= MIN_SCORE) {
if ((Neuroseg_Hit_Traced(&(chain->locseg), traced, z_scale) == FALSE) &&
(chain->locseg.seg.r1 < max_r) &&
(chain->locseg.seg.r2 < max_r)) {
//Initialize_Tracing(signal, chain, NULL, z_scale);
chain = Trace_Neuron2(signal, chain, BOTH, traced, z_scale, 500);
//Neurochain *chain_head = Neurochain_Head(chain);
chain_head = Neurochain_Remove_Overlap_Segs(chain);
chain_head = Neurochain_Remove_Turn_Ends(chain_head, 0.5);
/*
if (i == seed->size - 231) {
Print_Neurochain(chain_head);
}
*/
fp = fopen(chain_file_path, "w");
Neurochain_Fwrite(chain_head, fp);
fclose(fp);
if (Neurochain_Geolen(chain_head) >= min_chain_length) {
Write_Neurochain_Vrml(vrml_file_path, chain_head);
Neurochain_Erase_E(traced, chain_head, z_scale, 0,
Neurochain_Length(chain_head, FORWARD),
1.5, 0.0);
Neurochain_Label(canvas, chain_head, z_scale);
counter += Neurochain_Length(chain_head, FORWARD);
if (counter > 500) {
if (Is_Arg_Matched("-r")) {
Write_Stack((char *) trace_mask_path, traced);
}
if (Is_Arg_Matched("-r")) {
Write_Stack((char *) trace_file_path, canvas);
}
counter = 0;
}
}
}
}
Free_Neurochain(chain_head);
//Kill_Object_3d(obj);
}
Write_Stack((char *) trace_file_path, canvas);
if (Is_Arg_Matched("-r")) {
Write_Stack((char *) trace_mask_path, traced);
}
Kill_Geo3d_Scalar_Field(seed);
printf("Time passed: %lld\n", toc());
return 0;
}
int main(int argc, char* argv[])
{
char neuron_name[100];
if (argc == 1) {
strcpy(neuron_name, "fly_neuron");
} else {
strcpy(neuron_name, argv[1]);
}
char file_path[100];
sprintf(file_path, "../data/%s/mask.tif", neuron_name);
Stack *stack2 = Read_Stack(file_path);
Stack *stack3 = Copy_Stack(stack2);
sprintf(file_path, "../data/%s/blobmask.tif", neuron_name);
Stack *stack1 = Read_Stack(file_path);
Object_3d_List *objs = Stack_Find_Object_N(stack1, NULL, 1, 7, 26);
sprintf(file_path, "../data/%s/holeimg.tif", neuron_name);
Stack *hole_stack = Read_Stack(file_path);
int value;
int label = 2;
char id_file_path[100];
sprintf(id_file_path, "../data/%s/region_id.txt", neuron_name);
FILE *id_fp = fopen(id_file_path, "w");
while (objs != NULL) {
int hole_area = Stack_Foreground_Area_O(hole_stack, objs->data);
printf("%d / %lu\n", hole_area, objs->data->size);
//if (hole_area > (int) ((double) (objs->data->size) * 0.01)) {
if (hole_area > 100) {
value = 3;
} else {
value = 2;
}
if (objs->data->size + hole_area < TZ_PI * 10.0 * 10.0) {
TRACE("small object labeled");
}
fprintf(id_fp, "%d %d\n", label, value);
Stack_Draw_Object_Bw(stack3, objs->data, label++);
Stack_Draw_Object_Bw(stack2, objs->data, value);
objs = objs->next;
}
fprintf(id_fp, "-1 -1\n");
fclose(id_fp);
sprintf(file_path, "../data/%s/soma.tif", neuron_name);
Write_Stack(file_path, stack2);
printf("%s (2: arbor, 3: soma) created.\n", file_path);
sprintf(file_path, "../data/%s/region_label.tif", neuron_name);
Write_Stack(file_path, stack3);
printf("%s (one unique label for one region) created.\n", file_path);
Kill_Stack(stack1);
Kill_Stack(stack2);
Kill_Stack(stack3);
Kill_Stack(hole_stack);
return 0;
}
/**
* Find the background of a tif stack.
* Output : integer
* Input : stack file or bundle file.
*/
void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[])
{
if (nrhs < 1 || nrhs > 3)
mexErrMsgTxt("The function takes 1~3 arguments.");
if ( !mxIsChar(prhs[0]) )
mexErrMsgTxt("The argument must be a string");
if (nrhs == 2) {
if ( !tz_mxIsDoubleScalar(prhs[1]) )
mexErrMsgTxt("The second argument must be a doulbe scalar");
}
if (nrhs == 3) {
if ( !tz_mxIsDoubleScalar(prhs[2]) )
mexErrMsgTxt("The third argument must be a doulbe scalar");
}
char *filePath = mxArrayToString(prhs[0]);
Stack *stack = NULL;
if( strlen(filePath)>4 ) {
if( Is_Tiff(filePath) ) /* Read file */
stack = Read_Stack(filePath);
else if ( Is_Fbdf(filePath) ) { /* Read directory */
File_Bundle fb;
initfb(&fb);
if( Load_Fbdf(filePath,&fb) )
stack = Read_Stack_Planes(&fb);
freefb(&fb);
} else
mexErrMsgTxt("Unrecongnized file format.");
} else {
mexErrMsgTxt("Unrecongnized file format.");
}
if( stack==NULL )
mexErrMsgTxt("Unable to load the stack.");
int *hist,com;
int low,high;
if( stack->kind==GREY || stack->kind==GREY16 ) {
hist = Stack_Hist(stack);
if (nrhs == 1) {
low = hist[1];
high = hist[0]+hist[1]-1;
} else if (nrhs == 2) {
low = (int) (*mxGetPr(prhs[1]));
high = hist[0]+hist[1]-1;
} else {
low = (int) (*mxGetPr(prhs[1]));
high = (int) (*mxGetPr(prhs[2]));
}
printf("Pick threshold between %d and %d\n", low, high);
com = Hist_Most_Common(hist,low,high);
free(hist);
Kill_Stack(stack);
} else {
Kill_Stack(stack);
mexErrMsgTxt("Unsupported image format.");
}
uint8 *thre;
uint16 *thre16;
switch(stack->kind) {
case GREY:
plhs[0] = mxCreateNumericMatrix(1,1,mxUINT8_CLASS,mxREAL);
thre = (uint8 *) mxGetPr(plhs[0]);
*thre = com;
break;
case GREY16:
plhs[0] = mxCreateNumericMatrix(1,1,mxUINT16_CLASS,mxREAL);
thre16 = (uint16 *) mxGetPr(plhs[0]);
*thre16 = com;
break;
defaut:
Kill_Stack(stack);
mexErrMsgTxt("Unsupported image format.");
}
}
int main(int argc, char* argv[])
{
#if 0
Stack *stack = Read_Stack("../data/binimg.tif");
Set_Matlab_Path("/Applications/MATLAB74/bin/matlab");
Stack *dist = Stack_Bwdist(stack);
Stack* seeds = Stack_Local_Max(dist, NULL, STACK_LOCMAX_ALTER1);
Stack *out = Scale_Double_Stack((double *) dist->array, stack->width,
stack->height, stack->depth, GREY);
Translate_Stack(out, COLOR, 1);
Rgb_Color color;
Set_Color(&color, 255, 0, 0);
Stack_Label_Bwc(out, seeds, color);
Print_Stack_Info(dist);
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack *stack = Read_Stack("../data/benchmark/sphere_bw.tif");
//Stack *stack = Read_Stack("../data/sphere_data.tif");
//Stack_Not(stack, stack);
int i;
/*
uint8 *array = stack->array + 512 * 600;
for (i = 1; i < 512; i++) {
array[i] = 1;
}
*/
//stack->depth = 50;
/*
long int *label = (long int *) malloc(sizeof(long int) *
Stack_Voxel_Number(stack));
*/
tic();
Stack *out = Stack_Bwdist_L_U16(stack, NULL, 0);
uint16 *out_array = (uint16 *) out->array;
printf("%llu\n", toc());
//int *hist = Stack_Hist(out);
//Print_Int_Histogram(hist);
Stack *out2 = Stack_Bwdist_L(stack, NULL, NULL);
float *out2_array = (float *) out2->array;
int n = Stack_Voxel_Number(out);
int t = 0;
int x, y, z;
for (i = 0; i < n; i++) {
uint16 d2 = (uint16) out2_array[i];
if (out_array[i] != d2){
int area = stack->width * stack->height;
STACK_UTIL_COORD(i, stack->width, area, x, y, z);
printf("(%d %d %d)", x, y, z);
printf("%d %d %d\n", out_array[i], d2, stack->array[i]);
t++;
}
}
printf("%d error\n", t);
# if 0
//Translate_Stack(out, GREY, 1);
float *out_array = (float *) out->array;
int i;
int n = Stack_Voxel_Number(out);
/*
for (i = 0; i < n; i++) {
out_array[i] = sqrt(out_array[i]);
}
Stack *out2 = Scale_Float_Stack((float *)out->array, out->width, out->height,
out->depth, GREY);
*/
Stack *out2 = Make_Stack(GREY, out->width, out->height, out->depth);
for (i = 0; i < n; i++) {
out2->array[i] = (uint8) round(sqrt(out_array[i]));
}
Write_Stack("../data/test.tif", out2);
# endif
Write_Stack("../data/test.tif", out);
Kill_Stack(out);
Kill_Stack(out2);
#endif
#if 1
Stack *stack = Read_Stack("../data/system/29.tif");
Print_Stack_Info(stack);
tic();
Stack *out = Stack_Bwdist_L_U16P(stack, NULL, 0);
ptoc();
Stack *golden = Read_Stack("../data/system/29_dist2.tif");
printf("Checking result ...\n");
if (Stack_Identical(out, golden) == FALSE) {
printf("Result unmatched.\n");
} else {
printf("Good.\n");
}
#endif
return 0;
}
int main(int argc, char *argv[])
{
#if 0
Stack *stack = Read_Stack("../data/fly_neuron.tif");
Stretch_Stack_Value_Q(stack, 0.99);
Translate_Stack(stack, GREY, 1);
Write_Stack("../data/test.tif", stack);
Kill_Stack(stack);
#endif
#if 0
int idx1, idx2, width, height;
idx1 = 33332;
idx2 = 65535;
width = 111;
height = 112;
printf("%g\n", Stack_Util_Voxel_Distance(idx1, idx2, width, height));
int x1, y1, z1, x2, y2, z2;
Stack_Util_Coord(idx1, width, height, &x1, &y1, &z1);
Stack_Util_Coord(idx2, width, height, &x2, &y2, &z2);
printf("%d, %d, %d\n", x1 - x2, y1 - y2, z1 - z2);
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron.tif");
//Translate_Stack(stack, GREY16, 1);
Image *image = Proj_Stack_Zmax(stack);
Write_Image("../data/test.tif", image);
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron_a1_org.tif");
//stack = Crop_Stack(stack, 256, 256, 0, 512, 512, 170, NULL);
int i;
Stack stack2;
stack2.width = stack->width;
stack2.height = stack->height;
stack2.kind = stack->kind;
stack2.depth = 1;
for (i = 0; i < stack->depth; i++) {
stack2.array = stack->array + i * stack->width * stack->height;
//Stack *locmax = Stack_Locmax_Region(&stack2, 8);
Stack *locmax = Stack_Local_Max(&stack2, NULL, STACK_LOCMAX_SINGLE);
int *hist = Stack_Hist_M(&stack2, locmax);
int low, high;
Int_Histogram_Range(hist, &low, &high);
int thre = Int_Histogram_Triangle_Threshold(hist, low, high);
printf("Threshold: %d\n", thre);
Stack_Threshold_Binarize(&stack2, thre);
Kill_Stack(locmax);
free(hist);
}
//Stack_Bc_Autoadjust(result);
/*
Translate_Stack(stack, COLOR, 1);
Stack_Blend_Mc(stack, result, 0.1);
*/
Write_Stack("../data/test.tif", stack);
#endif
#if 1
Stack *stack = Read_Stack("../data/fly_neuron_crop.tif");
Filter_3d *filter = Gaussian_Filter_3d(1.0, 1.0, 0.5);
Stack *out = Filter_Stack(stack, filter);
Kill_FMatrix(filter)
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron_a2_org.tif");
Stack *locmax = Stack_Locmax_Region(stack, 18);
Stack *mask = Read_Stack("../data/fly_neuron_a2_org/threshold_s.tif");
//Stack_And(locmax, mask, locmax);
Object_3d_List *objs = Stack_Find_Object_N(locmax, NULL, 1, 0, 18);
Zero_Stack(locmax);
int objnum = 0;
while (objs != NULL) {
Object_3d *obj = objs->data;
Voxel_t center;
Object_3d_Central_Voxel(obj, center);
Set_Stack_Pixel(locmax, center[0], center[1], center[2], 0, 1);
objs = objs->next;
objnum++;
}
Write_Stack("../data/fly_neuron_a2_org/locmax.tif", locmax);
printf("objnum: %d\n", objnum);
U8Matrix mat;
mat.ndim = 3;
mat.dim[0] = stack->width;
mat.dim[1] = stack->height;
mat.dim[2] = stack->depth;
mat.array = locmax->array;
dim_type bdim[3];
bdim[0] = 7;
bdim[1] = 7;
bdim[2] = 5;
U8Matrix *mat2 = U8Matrix_Blocksum(&mat, bdim, NULL);
int offset[3];
offset[0] = bdim[0] / 2;
offset[1] = bdim[1] / 2;
offset[2] = bdim[2] / 2;
Crop_U8Matrix(mat2, offset, mat.dim, &mat);
Write_Stack("../data/fly_neuron_a2_org/locmax_sum.tif", locmax);
Stack_Threshold_Binarize(locmax, 6);
Stack *clear_stack = Stack_Majority_Filter_R(locmax, NULL, 26, 4);
Struct_Element *se = Make_Cuboid_Se(3, 3, 3);
Stack *dilate_stack = Stack_Dilate(clear_stack, NULL, se);
Stack *fill_stack = Stack_Fill_Hole_N(dilate_stack, NULL, 1, 4, NULL);
Kill_Stack(dilate_stack);
Stack_Not(fill_stack, fill_stack);
Stack_And(fill_stack, mask, mask);
Write_Stack("../data/test.tif", mask);
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron_t1.tif");
Stack *locmax = Stack_Locmax_Region(stack, 6);
Stack_Label_Objects_Ns(locmax, NULL, 1, 2, 3, 6);
int nvoxel = Stack_Voxel_Number(locmax);
int i;
int s[26];
for (i = 0; i < nvoxel; i++) {
if (locmax->array[i] < 3) {
locmax->array[i] = 0;
} else {
locmax->array[i] = 1;
printf("%u\n", stack->array[i]);
Stack_Neighbor_Sampling_I(stack, 6, i, -1, s);
iarray_print2(s, 6, 1);
}
}
//Stack *locmax = Stack_Local_Max(stack, NULL, STACK_LOCMAX_SINGLE);
Write_Stack("../data/test.tif", locmax);
#endif
#if 0
Stack *stack = Read_Stack("../data/fly_neuron_n1.tif");
Stack *stack2 = Flip_Stack_Y(stack, NULL);
Flip_Stack_Y(stack2, stack2);
if (!Stack_Identical(stack, stack2)) {
printf("bug found\n");
}
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/benchmark/L3_12bit.lsm", -1);
Mc_Stack_Grey16_To_8(stack, 3);
Write_Mc_Stack("../data/test.lsm", stack, "../data/benchmark/L3_12bit.lsm");
#endif
#if 0
//Stack *stack = Read_Stack("../data/C2-Slice06_R1_GR1_B1_L18.tif");
Stack *stack = Read_Stack("../data/fly_neuron_n1/traced.tif");
Print_Stack_Info(stack);
#endif
#if 0
Mc_Stack *stack = Make_Mc_Stack(GREY, 1024, 1024, 1024, 5);
/*
stack.width = 1024;
stack.height = 1024;
stack.depth = 1024;
stack.kind = GREY;
stack.nchannel = 5;
printf("%zd\n", ((size_t)stack.kind * stack.width * stack.height *
stack.depth * stack.nchannel));
*/
#endif
#if 0
Stack *stack = Make_Stack(GREY, 1, 1, 1);
printf("stack usage: %d\n", Stack_Usage());
uint8 *data = stack->array;
stack->array = NULL;
Kill_Stack(stack);
stack = Read_Stack("../data/benchmark/line.tif");
free(data);
printf("stack usage: %d\n", Stack_Usage());
#endif
#if 0
Stack *stack = Read_Stack("../data/test.tif");
int *hist = Stack_Hist(stack);
Print_Int_Histogram(hist);
#endif
#if 0
Stack *stack = Read_Stack("../data/benchmark/mouse_neuron_single/stack.tif");
Stack dst;
dst.text = "\0";
dst.array = stack->array;
Crop_Stack(stack, 0, 0, 0, stack->width - 100, stack->height - 100,
stack->depth - 30, &dst);
Write_Stack("../data/test.tif", &dst);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 5, 5, 3);
Zero_Stack(stack);
Set_Stack_Pixel(stack, 2, 2, 1, 0, 1.0);
Print_Stack_Value(stack);
Stack *out = Stack_Running_Max(stack, 0, NULL);
out = Stack_Running_Max(out, 1, out);
out = Stack_Running_Max(out, 2, out);
Print_Stack_Value(out);
#endif
#if 0
Stack *stack = Read_Stack("../data/benchmark/stack_graph/fork/fork.tif");
Stack *out = Stack_Running_Median(stack, 0, NULL);
Stack_Running_Median(out, 1, out);
//Stack_Running_Max(stack, 0, out);
//Stack_Running_Max(out, 1, out);
Write_Stack("../data/test.tif", out);
Stack *out2 = Stack_Running_Median(stack, 0, NULL);
Stack *out3 = Stack_Running_Median(out2, 1, NULL);
if (Stack_Identical(out, out3)) {
printf("Same in-place and out-place\n");
}
#endif
#if 0
Stack *stack = Read_Stack_U("../data/diadem_d1_147.xml");
printf("%d\n", Stack_Threshold_Quantile(stack, 0.9));
#endif
#if 0
const char *filepath = "/Users/zhaot/Data/Julie/All_tiled_nsyb5_Sum.lsm";
char filename[100];
fname(filepath, filename);
Mc_Stack *stack = Read_Mc_Stack(filepath, -1);
Print_Mc_Stack_Info(stack);
Mc_Stack *tmpstack = Make_Mc_Stack(stack->kind, stack->width, stack->height,
stack->depth / 8, stack->nchannel);
size_t channel_size = stack->kind * stack->width *stack->height
* stack->depth;
size_t channel_size2 = tmpstack->kind * tmpstack->width *tmpstack->height
* tmpstack->depth;
int i;
int k;
uint8_t *array = stack->array;
for (k = 0; k < 8; k++) {
int offset = 0;
int offset2 = 0;
for (i = 0; i < stack->nchannel; i++) {
memcpy(tmpstack->array + offset2, array + offset, channel_size2);
offset += channel_size;
offset2 += channel_size2;
}
array += channel_size2;
char outpath[500];
sprintf(outpath, "../data/test/%s_%03d.lsm", filename, k);
Write_Mc_Stack(outpath, tmpstack, filepath);
}
#endif
#if 0
Stack *stack = Index_Stack(GREY16, 5, 5, 1);
Set_Stack_Pixel(stack, 1, 1, 0, 0, 0);
Set_Stack_Pixel(stack, 1, 2, 0, 0, 0);
Print_Stack_Value(stack);
Stack *out = Stack_Neighbor_Median(stack, 8, NULL);
Print_Stack_Value(out);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 10, 10, 3);
Zero_Stack(stack);
Cuboid_I bound_box;
Set_Stack_Pixel(stack, 1, 1, 1, 0, 1);
Set_Stack_Pixel(stack, 1, 2, 1, 0, 1);
Set_Stack_Pixel(stack, 3, 1, 2, 0, 1);
Stack_Bound_Box(stack, &bound_box);
Print_Cuboid_I(&bound_box);
#endif
#if 0
Stack_Document *doc = Xml_Read_Stack_Document("../data/test.xml");
File_List *list = (File_List*) doc->ci;
Cuboid_I bound_box;
Stack_Bound_Box_F(list, &bound_box);
Print_Cuboid_I(&bound_box);
#endif
#if 0
Stack_Document *doc = Xml_Read_Stack_Document("../data/test.xml");
File_List *list = (File_List*) doc->ci;
Print_File_List(list);
Stack *stack = Read_Image_List_Bounded(list);
Stack *out = stack;
out = Stack_Region_Expand(stack, 8, 1, NULL);
out = Downsample_Stack(out, 4, 4, 0);
Write_Stack("../data/test.tif", out);
#endif
#if 0
Stack_Document *doc = Xml_Read_Stack_Document(
"../data/ting_example_stack/test.xml");
File_List *list = (File_List*) doc->ci;
Print_File_List(list);
int i;
for (i = 0; i < list->file_number; i++) {
Stack *stack = Read_Stack_U(list->file_path[i]);
Stack *ds = Downsample_Stack(stack, 39, 39, 0);
char file_path[500];
sprintf(file_path, "../data/ting_example_stack/thumbnails/tb%05d.tif", i);
Write_Stack(file_path, ds);
Free_Stack(stack);
}
#endif
#if 0
Stack *stack = Read_Stack("../data/test2.tif");
Stack_Threshold_Binarize(stack, 6);
Objlabel_Workspace ow;
STACK_OBJLABEL_OPEN_WORKSPACE(stack, (&ow));
Object_3d *obj = Stack_Find_Largest_Object_N(stack, ow.chord, 1, 26);
//Print_Object_3d(obj);
//printf("%llu\n", obj->size);
double vec[3];
Object_3d_Orientation(obj, vec, MAJOR_AXIS);
double center[3];
Object_3d_Centroid(obj, center);
darray_print2(vec, 3, 1);
double span[2] = {100000, -100000};
for (int i = 0; i < obj->size; i++) {
double proj = Geo3d_Dot_Product(vec[0], vec[1], vec[2],
(double) obj->voxels[i][0] - center[0],
(double) obj->voxels[i][1] - center[1],
(double) obj->voxels[i][2] - center[2]);
if (proj < span[0]) {
span[0] = proj;
}
if (proj > span[1]) {
span[1] = proj;
}
}
darray_print2(span, 2, 1);
double vec2[3];
Object_3d_Orientation(obj, vec2, PLANE_NORMAL);
darray_print2(vec2, 3, 1);
double span2[2] = {100000, -100000};
for (int i = 0; i < obj->size; i++) {
double proj = Geo3d_Dot_Product(vec2[0], vec2[1], vec2[2],
(double) obj->voxels[i][0] - center[0],
(double) obj->voxels[i][1] - center[1],
(double) obj->voxels[i][2] - center[2]);
if (proj < span2[0]) {
span2[0] = proj;
}
if (proj > span2[1]) {
span2[1] = proj;
}
}
darray_print2(span2, 2, 1);
double vec3[3];
Geo3d_Cross_Product(vec[0], vec[1], vec[2], vec2[0], vec2[1], vec2[2],
vec3, vec3+1, vec3+2);
double span3[2] = {100000, -100000};
int i;
for (i = 0; i < obj->size; i++) {
double proj = Geo3d_Dot_Product(vec3[0], vec3[1], vec3[2],
(double) obj->voxels[i][0] - center[0],
(double) obj->voxels[i][1] - center[1],
(double) obj->voxels[i][2] - center[2]);
if (proj < span3[0]) {
span3[0] = proj;
}
if (proj > span3[1]) {
span3[1] = proj;
}
}
darray_print2(span3, 2, 1);
coordinate_3d_t vertex[8];
for (i = 0; i < 8; i++) {
Coordinate_3d_Copy(vertex[i], center);
int j;
for (j = 0; j < 3; j++) {
vertex[i][j] +=
span[0] * vec[j] + span2[0] * vec2[j] + span3[0] * vec3[j];
}
}
for (i = 0; i < 3; i++) {
vertex[1][i] += (span[1] - span[0]) * vec[i];
vertex[2][i] += (span2[1] - span2[0]) * vec2[i];
vertex[3][i] += (span3[1] - span3[0]) * vec3[i];
vertex[4][i] = vertex[1][i] + (span2[1] - span2[0]) * vec2[i];
vertex[5][i] = vertex[2][i] + (span3[1] - span3[0]) * vec3[i];
vertex[6][i] = vertex[3][i] + (span[1] - span[0]) * vec[i];
vertex[7][i] = vertex[5][i] + (span[1] - span[0]) * vec[i];
}
FILE *fp = fopen("../data/test.swc", "w");
fprintf(fp, "%d %d %g %g %g %g %d\n", 1, 2, vertex[0][0], vertex[0][1],
vertex[0][2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 2, 2, vertex[1][0], vertex[1][1],
vertex[1][2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 3, 2, vertex[2][0], vertex[2][1],
vertex[2][2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 4, 2, vertex[3][0], vertex[3][1],
vertex[3][2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 5, 2, vertex[4][0], vertex[4][1],
vertex[4][2], 3.0, 2);
fprintf(fp, "%d %d %g %g %g %g %d\n", 6, 2, vertex[5][0], vertex[5][1],
vertex[5][2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 7, 2, vertex[6][0], vertex[6][1],
vertex[6][2], 3.0, 4);
fprintf(fp, "%d %d %g %g %g %g %d\n", 8, 2, vertex[7][0], vertex[7][1],
vertex[7][2], 3.0, 7);
fprintf(fp, "%d %d %g %g %g %g %d\n", 9, 2, vertex[4][0], vertex[4][1],
vertex[4][2], 3.0, 8);
fprintf(fp, "%d %d %g %g %g %g %d\n", 10, 2, vertex[4][0], vertex[4][1],
vertex[4][2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 11, 2, vertex[5][0], vertex[5][1],
vertex[5][2], 3.0, 8);
fprintf(fp, "%d %d %g %g %g %g %d\n", 12, 2, vertex[5][0], vertex[5][1],
vertex[5][2], 3.0, 4);
fprintf(fp, "%d %d %g %g %g %g %d\n", 13, 2, vertex[6][0], vertex[6][1],
vertex[6][2], 3.0, 2);
/*
Geo3d_Scalar_Field *field = Make_Geo3d_Scalar_Field(6);
field->points[0][0] = span[0] * vec[0] + center[0];
field->points[0][1] = span[0] * vec[1] + center[1];
field->points[0][2] = span[0] * vec[2] + center[2];
field->points[1][0] = span[1] * vec[0] + center[0];
field->points[1][1] = span[1] * vec[1] + center[1];
field->points[1][2] = span[1] * vec[2] + center[2];
field->points[2][0] = span2[0] * vec2[0] + center[0];
field->points[2][1] = span2[0] * vec2[1] + center[1];
field->points[2][2] = span2[0] * vec2[2] + center[2];
field->points[3][0] = span2[1] * vec2[0] + center[0];
field->points[3][1] = span2[1] * vec2[1] + center[1];
field->points[3][2] = span2[1] * vec2[2] + center[2];
field->points[4][0] = span3[0] * vec3[0] + center[0];
field->points[4][1] = span3[0] * vec3[1] + center[1];
field->points[4][2] = span3[0] * vec3[2] + center[2];
field->points[5][0] = span3[1] * vec3[0] + center[0];
field->points[5][1] = span3[1] * vec3[1] + center[1];
field->points[5][2] = span3[1] * vec3[2] + center[2];
coordinate_3d_t corner[2];
Geo3d_Scalar_Field_Boundbox(field, corner);
darray_print2(corner[0], 3, 1);
darray_print2(corner[1], 3, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 1, 2, corner[0][0], corner[0][1],
corner[0][2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 2, 2, corner[1][0], corner[0][1],
corner[0][2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 3, 2, corner[1][0], corner[1][1],
corner[0][2], 3.0, 2);
fprintf(fp, "%d %d %g %g %g %g %d\n", 4, 2, corner[0][0], corner[1][1],
corner[0][2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 5, 2, corner[0][0], corner[0][1],
corner[0][2], 3.0, 4);
fprintf(fp, "%d %d %g %g %g %g %d\n", 6, 2, corner[0][0], corner[0][1],
corner[1][2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 7, 2, corner[1][0], corner[0][1],
corner[1][2], 3.0, 6);
fprintf(fp, "%d %d %g %g %g %g %d\n", 8, 2, corner[1][0], corner[1][1],
corner[1][2], 3.0, 7);
fprintf(fp, "%d %d %g %g %g %g %d\n", 9, 2, corner[0][0], corner[1][1],
corner[1][2], 3.0, 8);
fprintf(fp, "%d %d %g %g %g %g %d\n", 10, 2, corner[0][0], corner[0][1],
corner[1][2], 3.0, 9);
fprintf(fp, "%d %d %g %g %g %g %d\n", 11, 2, corner[0][0], corner[0][1],
corner[1][2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 12, 2, corner[1][0], corner[0][1],
corner[1][2], 3.0, 2);
fprintf(fp, "%d %d %g %g %g %g %d\n", 13, 2, corner[1][0], corner[1][1],
corner[1][2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 14, 2, corner[0][0], corner[1][1],
corner[1][2], 3.0, 4);
*/
/*
fprintf(fp, "%d %d %g %g %g %g %d\n", 5, 2, corner[1][0], corner[1][1],
corner[1][2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 6, 2, corner[0][0], corner[1][1],
corner[1][2], 3.0, 6);
fprintf(fp, "%d %d %g %g %g %g %d\n", 7, 2, corner[1][0], corner[0][1],
corner[1][2], 3.0, 7);
fprintf(fp, "%d %d %g %g %g %g %d\n", 8, 2, corner[1][0], corner[1][1],
corner[0][2], 3.0, 7);
fprintf(fp, "%d %d %g %g %g %g %d\n", 12, 2, corner[1][0], corner[1][1],
corner[0][2], 3.0, 2);
fprintf(fp, "%d %d %g %g %g %g %d\n", 9, 2, corner[1][0], corner[1][1],
corner[1][2], 3.0, 6);
fprintf(fp, "%d %d %g %g %g %g %d\n", 10, 2, corner[0][0], corner[1][1],
corner[1][2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 11, 2, corner[1][0], corner[0][1],
corner[1][2], 3.0, 4);
fprintf(fp, "%d %d %g %g %g %g %d\n", 12, 2, corner[1][0], corner[1][1],
corner[0][2], 3.0, -1);
*/
fprintf(fp, "%d %d %g %g %g %g %d\n", 21, 2, span[0] * vec[0] + center[0],
span[0] * vec[1] + center[1], span[0] * vec[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 22, 2, span[1] * vec[0] + center[0],
span[1] * vec[1] + center[1], span[1] * vec[2] + center[2], 3.0, 21);
fprintf(fp, "%d %d %g %g %g %g %d\n", 23, 2, span2[0] * vec2[0] + center[0],
span2[0] * vec2[1] + center[1], span2[0] * vec2[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 24, 2, span2[1] * vec2[0] + center[0],
span2[1] * vec2[1] + center[1], span2[1] * vec2[2] + center[2], 3.0, 23);
fprintf(fp, "%d %d %g %g %g %g %d\n", 25, 2, span3[0] * vec3[0] + center[0],
span3[0] * vec3[1] + center[1], span3[0] * vec3[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 26, 2, span3[1] * vec3[0] + center[0],
span3[1] * vec3[1] + center[1], span3[1] * vec3[2] + center[2], 3.0, 25);
fclose(fp);
//double corner[6];
/*
FILE *fp = fopen("../data/test.swc", "w");
fprintf(fp, "%d %d %g %g %g %g %d\n", 1, 2, span[0] * vec[0] + center[0],
span[0] * vec[1] + center[1], span[0] * vec[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 2, 2, span[1] * vec[0] + center[0],
span[1] * vec[1] + center[1], span[1] * vec[2] + center[2], 3.0, 1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 3, 2, span2[0] * vec2[0] + center[0],
span2[0] * vec2[1] + center[1], span2[0] * vec2[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 4, 2, span2[1] * vec2[0] + center[0],
span2[1] * vec2[1] + center[1], span2[1] * vec2[2] + center[2], 3.0, 3);
fprintf(fp, "%d %d %g %g %g %g %d\n", 5, 2, span3[0] * vec3[0] + center[0],
span3[0] * vec3[1] + center[1], span3[0] * vec3[2] + center[2], 3.0, -1);
fprintf(fp, "%d %d %g %g %g %g %d\n", 6, 2, span3[1] * vec3[0] + center[0],
span3[1] * vec3[1] + center[1], span3[1] * vec3[2] + center[2], 3.0, 5);
fclose(fp);
*/
//calculate corners
//Draw the six line of the corners
/*
Stack *stack2 = Copy_Stack(stack);
Zero_Stack(stack2);
int i = 0;
for (i = 0; i < obj->size; i++) {
stack2->array[Stack_Util_Offset(obj->voxels[i][0], obj->voxels[i][1],
obj->voxels[i][2], stack->width, stack->height, stack->depth)] = 1;
}
Write_Stack("../data/test.tif", stack2);
*/
#endif
#if 0
Stack *stack = Read_Stack("../data/test2.tif");
Stack_Threshold_Binarize(stack, 6);
Objlabel_Workspace ow;
STACK_OBJLABEL_OPEN_WORKSPACE(stack, (&ow));
ow.conn = 26;
ow.init_chord = TRUE;
int obj_size = Stack_Label_Largest_Object_W(stack, 1, 2, &ow);
Object_3d *obj = Make_Object_3d(obj_size, ow.conn);
extract_object(ow.chord, ow.seed, obj);
//Print_Object_3d(obj);
/*
STACK_OBJLABEL_CLOSE_WORKSPACE((&ow));
Objlabel_Workspace *ow = New_Objlabel_Workspace();
ow->conn = 26;
ow->init_chord = TRUE;
STACK_OBJLABEL_OPEN_WORKSPACE(stack, ow);
Stack_Label_Largest_Object_W(stack, 1, 2, ow);
*/
Write_Stack("../data/test3.tif", stack);
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/test2.tif", -1);
Print_Mc_Stack_Info(stack);
size_t offset;
size_t voxelNumber = Mc_Stack_Voxel_Number(stack);
uint8_t* arrayc[3] = {NULL, NULL, NULL};
arrayc[0] = stack->array;
arrayc[1] = stack->array + voxelNumber;
arrayc[2] = stack->array + voxelNumber * 2;
for (offset = 0; offset < voxelNumber; ++offset) {
if ((arrayc[0][offset] != 128) || (arrayc[1][offset] != 6) ||
(arrayc[2][offset] != 0)) {
arrayc[0][offset] = 0;
arrayc[1][offset] = 0;
arrayc[2][offset] = 0;
}
}
Write_Mc_Stack("../data/test.tif", stack, NULL);
Kill_Mc_Stack(stack);
#endif
#if 0
Mc_Stack *stack = Read_Mc_Stack("../data/flyem/TEM/slice_figure/segmentation/selected_body.tif", -1);
Print_Mc_Stack_Info(stack);
size_t offset;
size_t voxelNumber = Mc_Stack_Voxel_Number(stack);
Stack *mask = Make_Stack(GREY, stack->width, stack->height, stack->depth);
uint8_t* arrayc[4] = {NULL, NULL, NULL, NULL};
int i;
for (i = 0; i < 4; ++i) {
arrayc[i] = stack->array + voxelNumber * i;
}
for (offset = 0; offset < voxelNumber; ++offset) {
if ((arrayc[0][offset] > 0) || (arrayc[1][offset] > 0) ||
(arrayc[2][offset] > 0) || (arrayc[3][offset] > 0)) {
mask->array[offset] = 1;
} else {
mask->array[offset] = 0;
}
}
mask = Downsample_Stack_Max(mask, 7, 7, 0, NULL);
Write_Stack("../data/test.tif", mask);
#endif
#if 0
Stack *stack = Read_Stack("../data/test2.tif");
size_t offset;
size_t voxelNumber = Stack_Voxel_Number(stack);
color_t *arrayc = (color_t*) stack->array;
for (offset = 0; offset < voxelNumber; ++offset) {
if ((arrayc[offset][0] != 128) || (arrayc[offset][1] != 6) ||
(arrayc[offset][2] != 0)) {
arrayc[offset][0] = 0;
arrayc[offset][1] = 0;
arrayc[offset][2] = 0;
}
}
Write_Stack("../data/test.tif", stack);
#endif
#if 0
Stack *stack = Read_Stack("../data/flyem/TEM/slice_figure/segmentation/selected_body_volume.tif");
Stack *out = Make_Stack(COLOR, stack->width, stack->height, stack->depth);
Zero_Stack(out);
Object_3d_List *objs = Stack_Find_Object_N(stack, NULL, 255, 0, 26);
Print_Object_3d_List_Compact(objs);
uint8_t color[] = {0, 200, 50, 200, 0, 0};
uint8_t *color2 = color;
while (objs != NULL) {
Object_3d *obj = objs->data;
Stack_Draw_Object_C(out, obj, color2[0], color2[1], color2[2]);
color2 += 3;
objs = objs->next;
break;
}
Write_Stack("../data/test.tif", out);
#endif
#if 0
//Stack *stack = Read_Stack("../data/benchmark/binary/2d/btrig2.tif");
Stack *stack = Make_Stack(GREY, 3, 3, 3);
One_Stack(stack);
//Zero_Stack(stack);
//Set_Stack_Pixel(stack, 0, 1, 1, 1, 1);
Set_Stack_Pixel(stack, 0, 1, 1, 1, 0);
Set_Stack_Pixel(stack, 0, 1, 1, 0, 0);
Set_Stack_Pixel(stack, 0, 0, 0, 0, 0);
Set_Stack_Pixel(stack, 0, 0, 2, 0, 0);
Set_Stack_Pixel(stack, 0, 2, 0, 0, 0);
Set_Stack_Pixel(stack, 0, 2, 2, 0, 0);
Set_Stack_Pixel(stack, 0, 0, 0, 2, 0);
Set_Stack_Pixel(stack, 0, 0, 2, 2, 0);
Set_Stack_Pixel(stack, 0, 2, 0, 2, 0);
Set_Stack_Pixel(stack, 0, 2, 2, 2, 0);
//Set_Stack_Pixel(stack, 0, 1, 1, 2, 0);
Stack_Graph_Workspace *sgw = New_Stack_Graph_Workspace();
//Default_Stack_Graph_Workspace(sgw);
sgw->signal_mask = stack;
Graph *graph = Stack_Graph_W(stack, sgw);
sgw->signal_mask = NULL;
//Print_Graph(graph);
//Graph_To_Dot_File(graph, "../data/test.dot");
if (Graph_Has_Hole(graph) == TRUE) {
printf("The graph has a hole.\n");
}
#endif
#if 0
Stack *stack = Read_Stack("../data/flyem/skeletonization/session3/T1_207.tif");
size_t voxel_number = Stack_Voxel_Number(stack);
size_t i;
for (i = 0; i < voxel_number; ++i) {
if (stack->array[i] == 1) {
stack->array[i] = 255;
}
}
Filter_3d *filter = Gaussian_Filter_3d(0.5, 0.5, 0.5);
Stack *out = Filter_Stack(stack, filter);
Write_Stack("../data/test2.tif", out);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 3, 3, 3);
Zero_Stack(stack);
Cuboid_I cuboid;
Cuboid_I_Set_S(&cuboid, 0, 0, 0, 4, 2, 3);
Cuboid_I_Label_Stack(&cuboid, 1, stack);
Print_Stack_Value(stack);
#endif
#if 0
Stack *stack = Make_Stack(GREY, 3, 3, 1);
Zero_Stack(stack);
Set_Stack_Pixel(stack, 1, 1, 0, 0, 1);
Print_Stack_Value(stack);
Stack *out = Downsample_Stack_Max(stack, 2, 2, 2, NULL);
Print_Stack_Value(out);
#endif
#if 0
double t[3] = {1, 2 * 256 + 12, 255 * 256};
printf("%g\n", Stack_Voxel_Weight_C(t));
#endif
#if 0
Stack *stack = Read_Stack_U("../data/vr/label.tif");
Stack_Binarize_Level(stack, 1);
Stack_Label_Large_Objects_N(stack, NULL, 1, 2, 2000, 4);
Stack_Threshold_Binarize(stack, 2);
Write_Stack("../data/vr/label1.tif", stack);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/vr/label.tif");
Stack_Binarize_Level(stack, 5);
Stack_Label_Large_Objects_N(stack, NULL, 1, 2, 5000, 4);
Stack_Threshold_Binarize(stack, 2);
Write_Stack("../data/vr/label5.tif", stack);
#endif
#if 0
Stack *stack = Read_Stack_U("../data/vr/original.tif");
/* Make mask */
Stack *mask = Make_Stack(GREY, Stack_Width(stack), Stack_Height(stack),
Stack_Depth(stack));
Zero_Stack(mask);
Stack *overallLabel = Copy_Stack(mask);
Stack *labelStack[5];
size_t voxelNumber = Stack_Voxel_Number(mask);
size_t k;
Struct_Element *se = Make_Disc_Se(5);
int i;
char filePath[100];
for (i = 0; i < 5; ++i) {
sprintf(filePath, "../data/vr/label%d.tif", i + 1);
labelStack[i] = Read_Stack_U(filePath);
//labelStack[i] = Stack_Erode_Fast(labelStack[i], NULL, se);
Stack_Or(mask, labelStack[i], mask);
for (k = 0; k < voxelNumber; ++k) {
if (labelStack[i]->array[k] == 1) {
overallLabel->array[k] = i + 1;
}
}
}
for (k = 0; k < voxelNumber; ++k) {
if (mask->array[k] == 1) {
mask->array[k] = SP_GROW_SOURCE;
}
}
Sp_Grow_Workspace *sgw = New_Sp_Grow_Workspace();
sgw->size = voxelNumber;
Sp_Grow_Workspace_Set_Mask(sgw, mask->array);
sgw->wf = Stack_Voxel_Weight_C;
sgw->sp_option = 1;
tic();
Int_Arraylist *path = Stack_Sp_Grow(stack, NULL, 0, NULL, 0, sgw);
printf("time: %llu\n", toc());
Kill_Int_Arraylist(path);
for (k = 0; k < voxelNumber; ++k) {
if (mask->array[k] == 0) {
int idx = (int) k;
while (overallLabel->array[idx] == 0) {
idx = sgw->path[idx];
}
int label = overallLabel->array[idx];
idx = (int) k;
while (overallLabel->array[idx] == 0) {
overallLabel->array[idx] = label;
idx = sgw->path[idx];
}
}
}
for (k = 0; k < voxelNumber; ++k) {
if (overallLabel->array[k] == 1 || overallLabel->array[k] == 5) {
overallLabel->array[k] = 0;
}
}
Write_Stack("../data/test.tif", overallLabel);
Kill_Stack(stack);
#endif
return 0;
}
int main(int argc, const char *argv[])
{
const char *result_dir = "/Users/zhaot/Work/V3D/neurolabi/data/align";
const char *image_dir = "/Users/zhaot/Data/nathan/2008-04-18";
char file_path[150];
char image_path[150];
char result_path[150];
char file1[100], file2[100];
char id[100];
fullpath(result_dir, "align_input.txt", file_path);
FILE *fp = fopen(file_path, "r");
while ((Read_Word(fp, file1, 0) > 0) &&
(Read_Word(fp, file2, 0) > 0)) {
align_id(file1, file2, id);
strcat(id, ".txt");
fullpath(result_dir, id, result_path);
if (!fexist(result_path)) {
printf("%s, %s\n", file1, file2);
fullpath(image_dir, file1, image_path);
Stack *stack1 = Read_Stack(image_path);
fullpath(image_dir, file2, image_path);
Stack *stack2 = Read_Stack(image_path);
// Stack_Threshold_Tp4(stack1, 0, 65535);
//Stack_Threshold_Tp4(stack2, 0, 65535);
int chopoff1 = estimate_chopoff(stack1);
printf("%d\n", chopoff1);
Stack *substack1 = Crop_Stack(stack1, 0, 0, chopoff1,
stack1->width, stack1->height,
stack1->depth - chopoff1, NULL);
int chopoff2 = estimate_chopoff(stack2);
printf("%d\n", chopoff2);
Stack *substack2 = Crop_Stack(stack2, 0, 0, chopoff2,
stack2->width, stack2->height,
stack2->depth - chopoff2, NULL);
float unnorm_maxcorr;
int offset[3];
int intv[] = {3, 3, 3};
float score = Align_Stack_MR_F(substack1, substack2, intv, 1, offset,
&unnorm_maxcorr);
if (score <= 0.0) {
printf("failed\n");
write_align_result(result_dir, file1, file2, NULL);
} else {
offset[2] += chopoff2;
printf("(%d, %d, %d): %g\n", offset[0], offset[1], offset[2], score);
write_align_result(result_dir, file1, file2, offset);
}
Kill_Stack(substack1);
Kill_Stack(substack2);
Kill_Stack(stack1);
Kill_Stack(stack2);
}
}
fclose(fp);
return 0;
}
int main()
{
/* Read stack */
Stack *stack = Read_Stack("../data/fly_neuron.tif");
double z_scale = 1.0;
/* New a bifold segment */
Local_Bifold_Neuroseg *locbn = New_Local_Bifold_Neuroseg();
/*
Set_Local_Bifold_Neuroseg(locbn, 2, 2, 2, 2, 30, 0.5,
TZ_PI_2, TZ_PI_2, -TZ_PI_2, 0,
461, 296, 144); //fly_neuron.tif
*/
Set_Local_Bifold_Neuroseg(locbn, 2, 2, 2, 2, 40, 0.5,
TZ_PI_2, TZ_PI_2, TZ_PI_2, TZ_PI_2,
290, 304, 112); //fly_neuron.tif
/*
Set_Local_Bifold_Neuroseg(locbn, 2, 2, 2, 2, 30, 0.5,
TZ_PI_2, TZ_PI_2, -TZ_PI_2, 0,
320, 164, 148); //fly_neuron.tif
*/
/*
Set_Local_Bifold_Neuroseg(locbn, 3, 3, 3, 3, 30, 0.5,
TZ_PI_2, TZ_PI_2, -TZ_PI_2, 0,
262, 136, 141); //fly_neuron2.tif
*/
/*
Set_Local_Bifold_Neuroseg(locbn, 3, 3, 3, 3, 30, 0.5,
TZ_PI_2, TZ_PI_2, -TZ_PI_2, 0,
236, 396, 143); //fly_neuron2.tif
*/
/* fit */
int var_index[LOCAL_BIFOLD_NEUROSEG_NPARAM];
int nvar = Local_Bifold_Neuroseg_Var_Mask_To_Index
(BIFOLD_NEUROSEG_VAR_MASK_R |
BIFOLD_NEUROSEG_VAR_MASK_KNOT |
BIFOLD_NEUROSEG_VAR_MASK_ORIENTATION2 |
BIFOLD_NEUROSEG_VAR_MASK_ORIENTATION, NEUROPOS_VAR_MASK_NONE, var_index);
Fit_Local_Bifold_Neuroseg(locbn, stack, var_index, nvar, z_scale, NULL);
Print_Local_Bifold_Neuroseg(locbn);
/* Generate field */
Geo3d_Scalar_Field *field = Local_Bifold_Neuroseg_Field(locbn, 1.0, NULL);
Delete_Local_Bifold_Neuroseg(locbn);
/* Draw it in a stack */
Stack *label = Make_Stack(FLOAT32, stack->width, stack->height, stack->depth);
Zero_Stack(label);
double coef[] = {0.1, 255.0};
double range[] = {0.0, 10000.0};
Geo3d_Scalar_Field_Draw_Stack(field, label, coef, range);
/* Turn the stack to GREY type */
Translate_Stack(label, GREY, 1);
/* Make canvas */
Translate_Stack(stack, COLOR, 1);
/* Label the canvas */
Stack_Label_Color(stack, label, 5.0, 1.0, label);
/* Save the stack */
Write_Stack("../data/test.tif", stack);
/* clean up */
Kill_Geo3d_Scalar_Field(field);
Kill_Stack(stack);
Kill_Stack(label);
return 0;
}
