/*
Median filter that only modifies a pixel when it significantly differs from the median of its 8-connected neighborhood that is weighted by the variance
@param img: input image
@param imgPara: struct with parameters
@param original: current height map
@param filterRadius: radius to define the 8-connected neighborhood
@param threshold: threshold to identify pixels that need to be modified
*/
Array * LocalMedianFilter_InclVar(RasterizedImage & img, ParaSet & imgPara, Array * original, int filterRadius, double threshold){
uint32 *orig = AUINT32(original);
Array *median = Make_Array_With_Shape(PLAIN_KIND, UINT32_TYPE, Coord2(original->dims[1], original->dims[0]));
uint32 *med = AUINT32(median);
Use_Extend_Boundary();
Frame * f = Make_Frame(original,Coord2(2*filterRadius+1,2*filterRadius+1),Coord2(filterRadius, filterRadius));
// Frame to compute the variance in intensity of the current grid element
Frame * varF = Make_Frame(img.GetImage(),Coord3(1, imgPara.radius,imgPara.radius),Coord3(0, 0, 0));
Histogram * varH = Make_Histogram(UVAL,256,ValU(1),ValU(0));
uint32 * data;
Place_Frame(f,0);
Place_Frame(varF, 0);
for (Dimn_Type y = 0; y <= img.GetHeight()-imgPara.radius; y += imgPara.radius){
for (Dimn_Type x = 0; x <= img.GetWidth()-imgPara.radius; x += imgPara.radius){
Indx_Type pHM = (y/imgPara.radius) * original->dims[0] + (x/imgPara.radius);
Place_Frame(f, pHM);
data = (uint32 *) Frame_Values(f);
std::vector<double> depths;
double sum = 0;
double n = 0;
for (int i = 0; i < AForm_Size(f); i++) {
Indx_Type p = Coord2IdxA(img.GetImage(), Coord3(data[i],y, x));
Place_Frame(varF, p);
Histagain_Array(varH,varF,0);
sum += Histogram_Variance(varH) * data[i];
n += Histogram_Variance(varH);
for (int j=0; j< floor(Histogram_Variance(varH)/10); j++) { // weight the current height with the variance
depths.push_back(data[i]);
}
}
double weightedMedian = VectorMedian(depths);
if (abs(orig[pHM] - weightedMedian) > threshold ) {
med[pHM] = floor(weightedMedian);
} else {
med[pHM] = orig[pHM];
}
}
}
Kill_Histogram(varH);
Kill_Frame(varF);
Kill_Frame(f);
return median;
}
void RasterizedImage::SetGrid(const int radius){
gridX_ = ceil ((double)realWidth_/(double)radius);
gridY_ = ceil ((double)realHeight_/(double)radius);
Use_Extend_Boundary();
Pad_Array_Inplace(*image_, Coord3(0, 0, 0), Coord3(depth_, gridY_*radius, gridX_*radius));
SetWidth((*image_)->dims[0]);
SetHeight((*image_)->dims[1]);
}
//default world:
// width = 1000, length = 1000, object at (500, 500)
World::World()
{
this->object = Coord3(500, 500, 0);
this->width = 1000;
this->length = 1000;
this->x_inc = 50;
this->y_inc = 100;
}
World::World(double obj_x, double obj_y, double obj_z, double width, double length)
{
this->object = Coord3(obj_x, obj_y, obj_z);
this->width = width;
this->length = length;
this->x_inc = 50;
this->y_inc = 100;
}
int Read_All_Channels(string name, int maxchans)
{ Tiff *tif;
int depth, height, width, chans;
int i;
if(strcmp(getSuffix(name), "tif")==0 || strcmp(getSuffix(name), "lsm")==0) {
tif = Open_Tiff(name,"r");
if (tif == NULL)
{ fprintf(stderr,"Cannot open file %s for reading\n",name);
exit (1);
}
Get_IFD_Shape(tif,&width,&height,&chans);
printf("width=%d height=%d chans=%d\n", width, height, chans);
if (chans < 2)
{ fprintf(stderr,"LSM %s does not at least 2 channels\n",name);
exit (1);
}
depth = 0;
while ( ! Tiff_EOF(tif))
{ int w, h, c;
Get_IFD_Shape(tif,&w,&h,&c);
if (w == width && h == height && c == chans)
{ for (i = 0; i < chans; i++)
if (Get_IFD_Channel_Type(tif,i) != UINT16_TYPE)
{ fprintf(stderr,"Channel %d of %s is not 16-bit)\n",i,name);
exit (1);
}
depth += 1;
}
Advance_Tiff(tif);
}
Rewind_Tiff(tif);
if (NumChans + chans > maxchans)
{ maxchans = 1.2*(NumChans+chans) + 20;
Images = (Array **) Guarded_Realloc(Images,sizeof(Array *)*maxchans,Program_Name());
}
for (i = NumChans; i < NumChans + chans; i++)
Images[i] = Make_Array_With_Shape(PLAIN_KIND,UINT16_TYPE,Coord3(depth,height,width));
depth = 0;
while ( ! Tiff_EOF(tif))
{ int w, h, c;
Get_IFD_Shape(tif,&w,&h,&c);
if (w == width && h == height && c == chans)
{ for (i = 0; i < chans; i++)
{ Array_Bundle plane = *(Images[NumChans+i]);
Get_IFD_Channel(tif,i,Get_Array_Plane(&plane,depth));
}
depth += 1;
}
Advance_Tiff(tif);
}
Close_Tiff(tif);
NumChans += chans;
return (maxchans);
} else if (strcmp(getSuffix(name), "raw")==0 || strcmp(getSuffix(name), "v3draw")==0) {
unsigned char* img;
long* sz;
img=0;
sz=0;
int rawLoadResult=loadRaw2Stack(name, &img, &sz, 2);
if (rawLoadResult!=0) {
fprintf(stderr, "Load of raw file failed\n");
exit(1);
}
if (sizeof(unsigned short)!=2) {
fprintf(stderr, "Read_All_Channels() making false assumption that unsigned short is size=2\n");
exit(1);
}
unsigned short* rawp=(unsigned short*)img;
width=sz[0];
height=sz[1];
depth=sz[2];
chans=sz[3];
printf("width=%d height=%d depth=%d chans=%d\n", width, height, depth, chans);
if (chans < 2)
{ fprintf(stderr,"File %s does not contain at least 2 channels\n",name);
exit (1);
}
if (NumChans + chans > maxchans)
{ maxchans = 1.2*(NumChans+chans) + 20;
Images = (Array **) Guarded_Realloc(Images,sizeof(Array *)*maxchans,Program_Name());
}
for (i = NumChans; i < NumChans + chans; i++) {
Images[i] = Make_Array_With_Shape(PLAIN_KIND,UINT16_TYPE,Coord3(depth,height,width));
{
int rx,ry,rz;
uint16 *v;
Indx_Type p;
v = AUINT16(Images[i]);
p = 0;
long oc=(i-NumChans)*depth*height*width;
for (rz=0;rz<depth;rz++) {
long oz = rz*height*width;
for (ry=0;ry<height;ry++) {
long oy = ry*width;
for (rx=0;rx<width;rx++) {
long offset=oc + oz + oy + rx;
unsigned short uv = *(rawp + offset);
v[p++] = uv;
}
}
}
}
}
NumChans += chans;
return (maxchans);
} else {
fprintf(stderr, "Do not recognize file suffix %s\n", getSuffix(name));
exit(1);
}
}
/*
Method that presents the image arr with a grid overlap
@param image: input image stack
@param imgPara: input parameter
@param name: name of the output file
@param arr: image which should be plotted
*/
void ShowArray(RasterizedImage & img, ParaSet & imgPara, char * name, Array * arr)
{
Dimn_Type x, y, z;
Array * a, * b;
if (imgPara.grid == false){
Write_Image((char *) name, arr, DONT_PRESS);
return;
}
// Conversion of the image arr into an RGB-Kind image
if (arr->type != UINT8_TYPE){
b = Copy_Array(arr);
Scale_Array_To_Range(b,ValU(0),ValU(255));
Convert_Array_Inplace(b,b->kind,UINT8_TYPE,8,0);
} else {
b = arr;
}
if (b->kind != RGB_KIND){
if (b == arr){
a = Convert_Array(b,RGB_KIND,b->type,b->scale,0);
} else {
a = Convert_Array_Inplace(b,RGB_KIND,b->type,b->scale,0);
}
} else {
a = b;
}
// Plotting of the image grid
if (a->ndims == 4)
for (z = 0; z < img.GetDepth(); z++){
for (y = 0; y < img.GetGridY(); y++) {
if (y % 50 == 0 && y != 0){
Draw_Line(a,&YELLOW,Coord3(z,y*imgPara.radius,0),Coord3(z,y*imgPara.radius,img.GetGridX()*imgPara.radius-1));
} else if (y % 10 == 0 && y != 0){
Draw_Line(a,&PURPLE,Coord3(z,y*imgPara.radius,0),Coord3(z,y*imgPara.radius,img.GetGridX()*imgPara.radius-1));
} else {
Draw_Line(a,&CYAN,Coord3(z,y*imgPara.radius,0),Coord3(z,y*imgPara.radius,img.GetGridX()*imgPara.radius-1));
}
for (x = 0; x < img.GetGridX(); x++){
if (x % 50 == 0 && x != 0){
Draw_Line(a,&YELLOW,Coord3(z,0,x*imgPara.radius),Coord3(z,img.GetGridY()*imgPara.radius-1,x*imgPara.radius));
} else if (x % 10 == 0 && x != 0){
Draw_Line(a,&PURPLE,Coord3(z,0,x*imgPara.radius),Coord3(z,img.GetGridY()*imgPara.radius-1,x*imgPara.radius));
} else {
Draw_Line(a,&CYAN,Coord3(z,0,x*imgPara.radius),Coord3(z,img.GetGridY()*imgPara.radius-1,x*imgPara.radius));
}
}
}
}
else{
for (y = 0; y < img.GetGridY(); y++){
if (y % 50 == 0 && y != 0){
Draw_Line(a,&YELLOW,Coord2(y*imgPara.radius,0),Coord2(y*imgPara.radius,img.GetGridX()*imgPara.radius-1));
} else if (y % 10 == 0 && y != 0){
Draw_Line(a,&PURPLE,Coord2(y*imgPara.radius,0),Coord2(y*imgPara.radius,img.GetGridX()*imgPara.radius-1));
} else{
Draw_Line(a,&CYAN,Coord2(y*imgPara.radius,0),Coord2(y*imgPara.radius,img.GetGridX()*imgPara.radius-1));
}
for (x = 0; x < img.GetGridX(); x++){
if (x % 50 == 0 && x != 0){
Draw_Line(a,&YELLOW,Coord2(0,x*imgPara.radius),Coord2(img.GetGridY()*imgPara.radius-1,x*imgPara.radius));
} else if (x % 10 == 0 && x != 0){
Draw_Line(a,&PURPLE,Coord2(0,x*imgPara.radius),Coord2(img.GetGridY()*imgPara.radius-1,x*imgPara.radius));
} else{
Draw_Line(a,&CYAN,Coord2(0,x*imgPara.radius),Coord2(img.GetGridY()*imgPara.radius-1,x*imgPara.radius));
}
}
}
}
Write_Image(name, a, DONT_PRESS);
if (arr != a)
Free_Array(a);
}
