예제 #1
0
void Print_Trace_Workspace(const Trace_Workspace *tw)
{
    printf("Maximum length: %d\n", tw->length);
    printf("Fit first? ");
    if (tw->fit_first == TRUE) {
        printf("Yes.\n");
    } else {
        printf("No.\n");
    }
    printf("Refit? ");
    if (tw->refit == TRUE) {
        printf("Yes.\n");
    } else {
        printf("No.\n");
    }
    printf("Break refit? ");
    if (tw->break_refit == TRUE) {
        printf("Yes.\n");
    } else {
        printf("No.\n");
    }
    printf("Tune ends? ");
    if (tw->tune_end == TRUE) {
        printf("Yes.\n");
    } else {
        printf("No.\n");
    }
    printf("Thresholding score option: %d; Threshold %g\n",
           tw->tscore_option, tw->min_score);
    printf("Minimal chain length: %g\n", tw->min_chain_length);
    printf("Trace step: %g\n", tw->trace_step);
    printf("Chain id: %d\n", tw->chain_id);
    printf("Tracing status: forward - %d, backward - %d\n",
           tw->trace_status[0], tw->trace_status[1]);
    printf("Tracing range: [%g %g] [%g %g] [%g %g]\n",
           tw->trace_range[0], tw->trace_range[3],
           tw->trace_range[1], tw->trace_range[4],
           tw->trace_range[2], tw->trace_range[5]);
    printf("Supervising stack: ");
    Print_Stack_Info(tw->sup_stack);
    printf("Tracing mask: ");
    Print_Stack_Info(tw->trace_mask);
    printf("Update tracing mask? ");
    if (tw->trace_mask_updating == TRUE) {
        printf("Yes.\n");
    } else {
        printf("No.\n");
    }
    printf("Canvas stack: ");
    Print_Stack_Info(tw->canvas);
    printf("Dynamic variables: %g %g %g %g %g\n",
           tw->dyvar[0], tw->dyvar[1], tw->dyvar[2], tw->dyvar[3], tw->dyvar[4]);
    printf("Resolution: %g um x %g um x %g um\n",
           tw->resolution[0], tw->resolution[1], tw->resolution[2]);
    printf("Saving path: %s\n", tw->save_path);
}
예제 #2
0
void Print_Locseg_Label_Workspace(const Locseg_Label_Workspace *ws)
{
  printf("Signal stack: ");
  Print_Stack_Info(ws->signal);
  printf("Option: %d\n", ws->option);
  printf("Flag: %d; Color: %u %u %u; Value %d\n", ws->flag,
	 ws->color[0], ws->color[1], ws->color[2], ws->value);
  printf("Swell: r * %g + %g (limit: %g)\n", ws->sratio, ws->sdiff, ws->slimit);
  printf("Range: [%d, %d], [%d, %d], [%d, %d]\n", ws->range[0], ws->range[3],
	 ws->range[1], ws->range[4], ws->range[2], ws->range[5]);
}
예제 #3
0
int main(int argc, char* argv[])
{
  /* save resolution information */
  double res[] = {0.7, 0.7, 1.6};
  darray_write("../data/mouse_neuron2_org.res", res, 3);

  int length;
  darray_read("../data/mouse_neuron2_org.res", res, &length);
  darray_print2(res, 3, 1);  
  
  double z_scale = res[0] / res[2];

  File_Bundle fb;
  fb.prefix = "/Users/zhaot/Data/neuromorph/mouse/ctrl/ctrl";
  fb.suffix = NULL;
  fb.num_width = 1;
  fb.first_num = 0;

  Stack *grey_stack = Read_Stack_Planes(&fb);
  Print_Stack_Info(grey_stack);

  Stack *resample_stack = Resample_Stack_Depth(grey_stack, NULL, z_scale);

  Write_Stack("../data/mouse_neuron2_org.tif", grey_stack);
  Write_Stack("../data/mouse_neuron2.tif", resample_stack);

  int stat = 
    symlink("../data/mouse_neuron2_org.tif", "../data/mouse_neuron2_org_org.tif");
  if (stat != 0) {
    perror(strerror(stat));
  }

  Kill_Stack(grey_stack);
  Kill_Stack(resample_stack);

  return 1;
}
예제 #4
0
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;
}
예제 #5
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;
}
예제 #6
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;
}
예제 #7
0
void Print_Stack_Tile(Stack_Tile *tile)
{
  Print_Stack_Info(tile->stack);
  printf("Offset: %g, %g, %g\n", tile->offset[0], tile->offset[1], 
	 tile->offset[2]);
}