#include "stdafx.h"
#include "PoroMediaDialogShare.h"
DS_cube* PoroMediaDialogShare::Dlg_Input_to_DS()
{
char int_file_name[1024];
DS_cube * cube = NULL;
char input_directory[1024], input_base_name[1024], work_directory[1024];
char output_name[1024];
//initialize all variables and directories that are needed
sprintf(input_directory, "%s", input_directory_name);
sprintf(input_base_name, "%s%s", input_directory, input_file_name_cut);
sprintf(work_directory, "%s", field_directory_work_str);
sprintf(output_name, "%s%s", work_directory, field_name_output_str);
{//write sample name to log
//char log_txt[512];
//sprintf(log_txt, "Input file selected: %s", input_base_name);
//write_to_log(log_txt);
write_to_log("Input file selected: %s", input_base_name);
write_to_log("Output: %s", output_name);
}
txt_field_progress.SetWindowText("Reading DATA...");
//create RAW_XY directory if needed
if ( (input_file_ext == INPUT_IS_BMP) || save_intermediate_results)
{
char raw_directory[512];
sprintf(raw_directory, "%sRAW_XY", work_directory);
if (!CreateDirectory(raw_directory,NULL)) //create a new RAW directory if needed
write_to_log("Message: 'RAW_XY' directory already exists, new one will not be created.");
}
//fill out Photoinfo structure
Photoinfo* info = new Photoinfo;
info->type = input_file_ext;
info->startofx = (unsigned short)field_start_X_int;
info->startofy = (unsigned short)field_start_Y_int;
info->startofz = (unsigned short)field_start_slice_int;
info->sizeofx = (unsigned short)field_width_X_int;
info->sizeofy = (unsigned short)field_width_Y_int;
info->sizeofz = (unsigned short)field_width_slices_int;
//init file base name
sprintf(int_file_name, "%sRAW_XY\\%s", work_directory, field_name_output_str);
//if image type is BMP, convert to RAW
if ( (info->type == INPUT_IS_BMP) && (!stop_request))
{
sprintf(info->bmp_prefix,"%s", input_base_name);
sprintf(info->raw_prefix,"%sRAW_XY\\%s(%d_%d_%d)", work_directory, field_name_output_str, info->sizeofx, info->sizeofy, info->sizeofz);
txt_field_progress.SetWindowText("Converting .BMP images to RAW format...");
write_to_log("Converting .BMP images to RAW format...");
if ( !extract(info, (void*) this) )
{
write_to_log("BMP to RAW conversion failed.");
txt_field_progress.SetWindowText("BMP images to RAW conversion failed.");
return NULL;
}
write_to_log("BMP to RAW conversion successful.");
}
//
// if image type is BMP, RAW, or RAW_STACK, determine threshold and binarize
//
if ( (info->type == INPUT_IS_BMP) || (info->type == INPUT_IS_RAW) || (info->type == INPUT_IS_RAW_STACK) )
{
//if input was BMP, then there already is a raw_prefix from conversion, otherwise the raw prefix is the input
if (info->type != INPUT_IS_BMP)
sprintf(info->raw_prefix, "%s", input_base_name);
else
sprintf(info->raw_prefix, "%s.stack.raw", info->raw_prefix);
cube = new DS_cube(info, (void*) this);;
}
if (info)
delete info;
return cube;
}
/*********************************************************
Converts the Dialog Object to a 3D Binary Data Cube
*********************************************************/
DS_1b_cube* PoroMediaDialogShare::Dlg_Input_to_cDS()
{
int invert = 0, manual = 0;
int thres;
char int_file_name[1024];
DS_1b_cube *orig_cube = 0;
char input_directory[1024], input_base_name[1024], work_directory[1024];
//initialize all variables and directories that are needed
sprintf(input_directory, "%s", input_directory_name);
sprintf(input_base_name, "%s%s", input_directory, input_file_name);
sprintf(work_directory, "%s", field_directory_work_str);
//write sample name to log
write_to_log("Input file selected: %s", input_base_name);
txt_field_progress.SetWindowText("Reading DATA...");
//create RAW_XY directory if needed
if ( (input_file_ext == INPUT_IS_BMP) || (save_intermediate_results==true) )
//if ( (input_file_ext == INPUT_IS_BMP) & (save_intermediate_results==true) )
{
char raw_directory[512];
sprintf(raw_directory, "%sRAW_XY", work_directory);
if (!CreateDirectory(raw_directory,NULL)) //create a new RAW directory if needed
{
write_to_log("Message: 'RAW_XY' directory already exists, new one will not be created.");
}
}
//if we want to save the binarized input, make sure the BIN_XY directory exists
if ( is_control_enabled(FILESAVE_CONTROLS) && (check_save_cbin_stack.GetCheck() || save_intermediate_results) )
{
char bin_directory[512];
sprintf(bin_directory, "%sBIN_XY", work_directory);
if ( !CreateDirectory(bin_directory,NULL) ) //create a new BIN directory if needed
{
write_to_log("Message: 'BIN' directory already exists, new one will not be created.");
}
}
//fill out Photoinfo structure
Photoinfo *info = new Photoinfo;
info->type = input_file_ext;
info->startofx = (unsigned short)field_start_X_int;
info->startofy = (unsigned short)field_start_Y_int;
info->startofz = (unsigned short)field_start_slice_int;
info->sizeofx = (unsigned short)field_width_X_int;
info->sizeofy = (unsigned short)field_width_Y_int;
info->sizeofz = (unsigned short)field_width_slices_int;
//init file base name
sprintf(int_file_name, "%sRAW_XY\\%s", work_directory, field_name_output_str);
//if image type is BMP, convert to RAW
if ( (info->type == INPUT_IS_BMP) && (!stop_request))
{
sprintf(info->bmp_prefix,"%s", input_base_name);
sprintf(info->raw_prefix,"%sRAW_XY\\%s(%d_%d_%d)", work_directory,
field_name_output_str, info->sizeofx, info->sizeofy, info->sizeofz);
txt_field_progress.SetWindowText("Converting .BMP images to RAW format...");
write_to_log("Converting .BMP images to RAW format...");
if ( !extract(info, (void*) this) )
{
write_to_log("BMP to RAW conversion failed.");
txt_field_progress.SetWindowText("BMP images to RAW conversion failed.");
return NULL;
}
write_to_log("BMP to RAW conversion successful.");
}
//
// if image type is BMP, RAW, or RAW_STACK, determine threshold and binarize
//
if ( (info->type == INPUT_IS_BMP) || (info->type == INPUT_IS_RAW) || (info->type == INPUT_IS_RAW_STACK) )
{
//if input was BMP, then there already is a raw_prefix from conversion, otherwise the raw prefix is the input
if (info->type != INPUT_IS_BMP)
{
sprintf(info->raw_prefix, "%s", input_base_name);
}
else
{
sprintf(info->raw_prefix, "%s.stack.raw", info->raw_prefix);
}
/////////////////////////////////////////////////
//do any RAW filters here
/////////////////////////////////////////////////
DS_cube *cube = NULL;
//contrast
if (is_control_enabled(FILTER_CONTROLS) && check_filter_contrast_enable.GetCheck() && (!stop_request) )
{
//log
write_to_log( "filtering: contrast enhancement");
if ( cube == NULL )
{
cube = new DS_cube(info, (void*) this);
}
//ds_median_w_center(cube, (void*) this);
//sprintf(file_out, "%sRAW_XY//%s_Med(%d_%d_%d).stack.raw", work_directory, field_name_output_str, cube->wX, cube->wY, cube->wZ);
txt_field_progress.SetWindowText("Contrast filtering...");
contrast(cube, (unsigned char)filter_contrast_percentage, (void*) this);
if (is_control_enabled(FILESAVE_CONTROLS) && save_intermediate_results && (!stop_request))
{
char file_out [512];
txt_field_progress.SetWindowText("Saving contrast filter results...");
sprintf(file_out, "%s_Contr", int_file_name);
sprintf(int_file_name, "%s", file_out); //set resulting name
sprintf(file_out, "%s(%d_%d_%d).stack.raw", int_file_name, cube->wX, cube->wY, cube->wZ);
cube->write_to_RAW_STACK(file_out);
}
}
//convolve
if (is_control_enabled(FILTER_CONTROLS) && check_filter_convolve_enable.GetCheck() && !stop_request )
{
//log it
write_to_log("filtering: convolve filter");
if ( cube == NULL )
{
cube = new DS_cube(info, (void*) this);
}
//{
// bypass4(cube, (void*)this, ""); //histogram
// //bypass5(cube, (void*)this); //unwrap
////delete RAW cube
// if (cube)
// delete cube;
// return 0;
//}
txt_field_progress.SetWindowText("Convolve filtering...");
if (filter_convolve_type == 0 || filter_convolve_type == 1) //median
{
convolve_filter_median(cube, (void*) this);
}
else if (filter_convolve_type == 6)
{
//convolve_downsample(cube, (void*) this); //downsample (beta)
//unsigned short int mask_size = (short int)(filter_convolve_radius) + 1;
//cube->resize2(mask_size, mask_size, mask_size); //downsample
convolve_anisotropic_diffusion(cube, (void*) this); //aniso
//convolve_sobel_edge_detect(cube, (void*) this); //edge detector
//convolve_threshold(cube, (void*) this); //thresholding
}
else
{//all other cases
convolve_filter(cube, (void*) this);
}
//histogram result
{
char file_out [512];
sprintf(file_out, "%s_Conv%d_%.1f", int_file_name, filter_convolve_type, filter_convolve_radius);
sprintf(file_out, "%s(%d_%d_%d).stack.raw", file_out, cube->wX, cube->wY, cube->wZ);
bypass4(cube, (void*) this, file_out);
}
if ( !filter_convolve_savebounds && !stop_request ) //resize cube after convolve
{
unsigned short int mask_radius = (short int)(filter_convolve_radius);
cube->resize_enveloppe(mask_radius, mask_radius, mask_radius);
}
if (is_control_enabled(FILESAVE_CONTROLS) && save_intermediate_results && (!stop_request))
{
char file_out [512];
txt_field_progress.SetWindowText("Saving convolve filter results...");
sprintf(file_out, "%s_Conv%d_%.1f", int_file_name, filter_convolve_type, filter_convolve_radius);
sprintf(int_file_name, "%s", file_out); //set resulting name
sprintf(file_out, "%s(%d_%d_%d).stack.raw", int_file_name, cube->wX, cube->wY, cube->wZ);
cube->write_to_RAW_STACK(file_out);
txt_field_progress.SetWindowText("Saving convolve filter results... Done!");
}
}
//anisotropic diff
if (is_control_enabled(FILTER_CONTROLS) && check_filter_aniso_enable.GetCheck() && !stop_request )
{
char win_txt[512];
write_to_log("filtering: anisotropic diffusion");
if ( cube == NULL ) //check if 'cube' has been allocated, if not, allocate it!
{
cube = new DS_cube(info, (void*) this);
}
sprintf(win_txt, "Anisotropic Diffusion (%d steps)..", filter_aniso_iterations);
txt_field_progress.SetWindowText(win_txt);
if (filter_aniso_fast)
{
//anisotropic_diffusion2D_3planes_extended(cube, (void*)this);
}
else
{
convolve_anisotropic_diffusion(cube, (void*) this);
}
sprintf(win_txt, "Anisotropic Diffusion (%d steps).... done", filter_aniso_iterations);
txt_field_progress.SetWindowText(win_txt);
if ( !filter_aniso_savebounds && !stop_request ) //resize cube after aniso
{
unsigned short int mask_radius = (short int)(filter_aniso_radius);
cube->resize_enveloppe(mask_radius, mask_radius, mask_radius);
}
if (is_control_enabled(FILESAVE_CONTROLS) && save_intermediate_results && (!stop_request) && (filter_aniso_K != 1)) //K=1 special case to perform histogramming only
{
char file_out [512];
txt_field_progress.SetWindowText("Saving anisotropic diffusion filter results...");
sprintf(file_out, "%s_Aniso", int_file_name);
sprintf(int_file_name, "%s", file_out);
//sprintf(file_out, "%s(%d_%d_%d).stack.raw", int_file_name, cube->wX, cube->wY, cube->wZ);
char diff_coeff;
switch (filter_aniso_diff_coef) // 0 = 1/[1+]^2, 1 = exp^2, 2 = exp^4, 3 = exp^n
{
case 0:
diff_coeff = '1';
break;
case 1:
diff_coeff = 'e';
break;
case 2:
diff_coeff = '4';
break;
default:
diff_coeff = 'n';
break;
}
sprintf(file_out, "%s_%c_K%dI%dm%d(%d_%d_%d).stack.raw", int_file_name, \
diff_coeff, (unsigned char)filter_aniso_K, (unsigned char)filter_aniso_iterations, \
(unsigned char)filter_aniso_midpoint, cube->wX, cube->wY, cube->wZ);
cube->write_to_RAW_STACK(file_out);
}
}
//remove
// convert RAW file to BIN using thershold, unless skip is specified
if ( skip_binarization && !stop_request )
{
write_to_log("PoroMedia: Binarization was skipped.");
//clean up
delete cube;
delete info;
//return NULL since nothing was binarized
return NULL;
}
//determine THRESHOLD, manual or auto
if (!stop_request)
{
int threshold_method = combo_threshold_method.GetCurSel();
if(threshold_method == 0)
{//manual threshold
thres = field_manual_threshold_int;
manual = 1;
invert = ( check_image_is_inverted.GetCheck() ) ? ( 1 ) : ( 0 );
}
else
{//automatic threshold
txt_field_progress.SetWindowText("Determining threshold automatically...");
Log_value result;
if ( check_image_is_inverted.GetCheck() )
{
invert = 1;
result = threshold(info, cube, 0, 50, 254, threshold_method);
thres = result.value;
}
else
{
invert = 0;
result = threshold(info, cube, 0, 0, 192, threshold_method);
thres = result.value;
}
//update GUI threshold displayed
SetIntValField(&(field_manual_threshold), thres);
field_manual_threshold_int = thres;
}
}
if (!stop_request)
{
txt_field_progress.SetWindowText("Converting RAW images to BIN format...");
orig_cube = binarize(info, cube, this);
write_to_log("Message: RAW to BIN conversion successful.");
}
//delete RAW cube
if (cube)
{
delete cube;
}
}
//already binarized
else if (!stop_request)
{
txt_field_progress.SetWindowText("Reading BIN input into memory...");
//input is already binary, so just place BIN file into compressed DS
orig_cube = new DS_1b_cube(input_base_name, info->type, info->startofz, info->sizeofz, info->sizeofy, info->sizeofx);
if (!orig_cube->data)
{
write_to_log("Input Scan: Invalid file extension detected.");
return NULL;
}
}
/////////////////////////////////////////////////
//now we have a 1b_cube in 'orig_cube', so do any BINARY filters here
/////////////////////////////////////////////////
sprintf(int_file_name, "%sBIN_XY\\%s", work_directory, field_name_output_str);
if (is_control_enabled(FILTER_CONTROLS) && check_filter_voxrem_enable.GetCheck() && (!stop_request))
{ //isolated voxel removal
char file_out [512];
DS_1b_cube * temp;
IsolatedVoxRemover * voxremover;
//calc unit voxel volume
float unit_vox_vol = field_pixel_size_float * field_pixel_size_float * field_pixel_size_float;
//for pores
if (filter_voxrem_removal_run_4_pore)
{
filter_voxrem_pore_vox_vol = (long)(filter_voxrem_pore_um_vol/unit_vox_vol + .5); //calc total voxel volume and round it
temp = orig_cube;
voxremover = new IsolatedVoxRemover(orig_cube);
//file where the stats of spec removal will be place
if (is_control_enabled(FILESAVE_CONTROLS) && save_intermediate_results)
{
sprintf(file_out, "%s_SpecPorRem", int_file_name);
sprintf(int_file_name, "%s", file_out);
sprintf(file_out, "%s(%d_%d_%d)_stats.txt", int_file_name, orig_cube->wX, orig_cube->wY, orig_cube->wZ);
}
else
{
file_out[0] = '\0';
}
txt_field_progress.SetWindowText("Running specal removal on pores...");
write_to_log("PoroMedia: now starting pore voxel removal.");
orig_cube = voxremover->Run_Vox_Remover(file_out, 0 /*to remove*/, filter_voxrem_pore_vox_vol, (void*) this);
write_to_log("PoroMedia: done with pore voxel removal");
if (is_control_enabled(FILESAVE_CONTROLS) && save_intermediate_results && (!filter_voxrem_removal_run_4_fiber) && (!stop_request) )
{
sprintf(file_out, "%s_SpecPorRem", int_file_name);
sprintf(int_file_name, "%s", file_out);
sprintf(file_out, "%s(%d_%d_%d).stack.cbin", int_file_name, orig_cube->wX, orig_cube->wY, orig_cube->wZ);
orig_cube->writeToFile(file_out);
}
delete voxremover;
delete temp;
}
//for fibers
if (filter_voxrem_removal_run_4_fiber && (!stop_request))
{
filter_voxrem_fiber_vox_vol = (long)(filter_voxrem_fiber_um_vol/unit_vox_vol + .5); //calc total voxel volume and round it
temp = orig_cube;
voxremover = new IsolatedVoxRemover(orig_cube);
//file where the stats of spec removal will be place
if (is_control_enabled(FILESAVE_CONTROLS) && save_intermediate_results)
{
sprintf(file_out, "%s_SpecFibRem", int_file_name);
sprintf(int_file_name, "%s", file_out);
sprintf(file_out, "%s(%d_%d_%d)_stats.txt", int_file_name, orig_cube->wX, orig_cube->wY, orig_cube->wZ);
}
else
{
file_out[0] = '\0';
}
txt_field_progress.SetWindowText("Running specal removal on fibers...");
write_to_log("PoroMedia: now starting fiber voxel removal.");
orig_cube = voxremover->Run_Vox_Remover(file_out, 1 /*to remove*/, filter_voxrem_fiber_vox_vol, (void*) this);
write_to_log("PoroMedia: done with fiber voxel removal");
if (is_control_enabled(FILESAVE_CONTROLS) && save_intermediate_results && (!filter_voxrem_removal_run_4_pore) )
{
sprintf(file_out, "%s_SpecFibRem", int_file_name);
sprintf(int_file_name, "%s", file_out);
sprintf(file_out, "%s(%d_%d_%d).stack.cbin", int_file_name, orig_cube->wX, orig_cube->wY, orig_cube->wZ);
}
else
{
sprintf(file_out, "%s_SpecPor&FibRem", int_file_name);
sprintf(int_file_name, "%s", file_out);
sprintf(file_out, "%s(%d_%d_%d).stack.cbin", int_file_name, orig_cube->wX, orig_cube->wY, orig_cube->wZ);
}
if (is_control_enabled(FILESAVE_CONTROLS) && save_intermediate_results && (!stop_request))
{
orig_cube->writeToFile(file_out);
}
delete voxremover;
delete temp;
}
txt_field_progress.SetWindowText("Done with specal removal.");
}
if (is_control_enabled(FILTER_CONTROLS) && check_filter_close_enable.GetCheck() && (!stop_request))
{ //close filter
write_to_log( "PoroMedia: now starting %d iterations of Close filter...", filter_close_iterations );
close_filter(orig_cube, filter_close_neighs, filter_close_extended, filter_close_iterations, (void*)this);
write_to_log("PoroMedia: done with Close filter.");
if (is_control_enabled(FILESAVE_CONTROLS) && save_intermediate_results && (!stop_request))
{
char file_out [512];
sprintf(file_out, "%s_%dClose", filter_close_iterations, int_file_name);
sprintf(int_file_name, "%s", file_out);
sprintf(file_out, "%s(%d_%d_%d).stack.cbin", int_file_name, orig_cube->wX, orig_cube->wY, orig_cube->wZ);
txt_field_progress.SetWindowText("Saving Close filter results...");
orig_cube->writeToFile(file_out);
}
txt_field_progress.SetWindowText("Done with Close filter.");
}
//****************************************************
// if we want to save bin conversion to a .stack.cbin file
//****************************************************
if (is_control_enabled(FILESAVE_CONTROLS) && check_save_cbin_stack.GetCheck() && (!stop_request))
{
char outfile[512];
sprintf(outfile,"%sBIN_XY\\%s(%d_%d_%d).stack.cbin", work_directory,
field_name_output_str, info->sizeofx, info->sizeofy, info->sizeofz);
if (!orig_cube->writeToFile(outfile))
{
write_to_log("PoroMedia common: error: cannot open output file %s", outfile);
return NULL;
}
}
if ( info )
{
delete info;
}
if (stop_request)
{
StopConfirm();
//txt_field_progress.SetWindowText("Run stopped successfully.");
if (orig_cube)
{
delete orig_cube;
}
//stop_request = false;
return NULL;
}
else
{
return orig_cube;
}
}