void Output_Neurons(int numneur, Region **neurons, int do_brighten)
{ Array *stack, *proj;
int i, k;
#ifdef PROGRESS
printf("\nGenerating %d individual neuron stacks\n",numneur);
fflush(stdout);
#endif
stack = Make_Array(RGB_KIND,UINT16_TYPE,3,Images[0]->dims);
proj = Make_Array(RGB_KIND,UINT16_TYPE,2,Images[0]->dims);
for (i = 0; i < numneur; i++)
{ Array_Op_Scalar(stack,SET_OP,UVAL,VALU(0));
for (k = 0; k < NumChans; k++)
{ Array_Bundle plane = *stack;
Draw_Region_Image(Get_Array_Plane(&plane,k%3),Images[k],neurons[i]);
}
if (do_brighten)
Scale_Array_To_Range(stack,VALU(0),VALU(4095));
if (!Is_Arg_Matched("-pj"))
{ sprintf(NameBuf,"%s/%s.neuron%d.tif",RezFolder,CoreName,i);
Write_Image(NameBuf,stack,LZW_PRESS);
}
#ifdef PROGRESS
printf("*"); fflush(stdout);
#endif
Z_Projection(stack,proj);
sprintf(NameBuf,"%s/%s.PR.neuron%d.tif",RezFolder,CoreName,i);
Write_Image(NameBuf,proj,LZW_PRESS);
}
// Kill_Array(proj); these are causing a glib.c memory error in Linux
// Kill_Array(stack);
#ifdef PROGRESS
printf("\n"); fflush(stdout);
#endif
}
void RasterizedImage::ScaleTo8bit(){
Scale_Array_To_Range((*image_),ValU(0),ValU(255));
Convert_Array_Inplace((*image_),PLAIN_KIND,UINT8_TYPE,8,0);
}
/*
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);
}