/**
* 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.");
}
}
bool ZStackBinarizer::binarize(Stack *stack)
{
if (stack == NULL) {
return false;
}
int threshold = m_threshold;
int *hist = NULL;
Stack *refStack = C_Stack::clone(m_reference);
if (refStack == NULL) {
refStack = stack;
}
int low = m_lowerBound;
int high = m_upperBound;
switch (m_method) {
case BM_RC_THRESHOLD:
case BM_STABLE_POINT:
case BM_TRIANGLE:
hist = Stack_Hist(refStack);
break;
case BM_LOCMAX:
hist = computeLocmaxHist(refStack);
break;
default:
break;
}
if (hist != NULL) {
if (m_lowerBound < 0) {
low = Int_Histogram_Min(hist);
}
if (m_upperBound < 0) {
high = Int_Histogram_Max(hist);
}
}
if (low == high && hist != NULL) {
BINARIZE_CLEAN
return false;
}
/**
* 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/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, 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;
}