IppStatus PrintOutputImages(const Image2D &image_in, const Image2D &image_bpass, const Image2D &image_localmax,
const Params &Parameters, const int framenumber, const int stacknumber,
FIMULTIBITMAP *filt_imagestack, FIMULTIBITMAP *over_imagestack)
{
IppStatus status;
Image2D image_out(image_in.get_length(), image_in.get_width());
Image2D image_overlay(image_in.get_length(), image_in.get_width());
Image2D centerpoints(image_in.get_length(), image_in.get_width());
Ipp32f brightness = 75;
//scale points to brightness
status = ippiMulC_32f_C1R(image_localmax.get_image2D(), image_localmax.get_stepsize(), brightness,
centerpoints.get_image2D(), centerpoints.get_stepsize(), image_localmax.get_ROIfull());
//convert and save files as TIFFs
status = ippiAdd_32f_C1R(
image_bpass.get_image2D(), image_bpass.get_stepsize(),
centerpoints.get_image2D(), centerpoints.get_stepsize(),
image_out.get_image2D(), image_out.get_stepsize(),
image_out.get_ROIfull());
status = ippiAdd_32f_C1R(
image_in.get_image2D(), image_in.get_stepsize(),
centerpoints.get_image2D(), centerpoints.get_stepsize(),
image_overlay.get_image2D(), image_overlay.get_stepsize(),
image_in.get_ROIfull());
status = IPP_to_TIFF(image_overlay, over_imagestack);
status = IPP_to_TIFF(image_out, filt_imagestack);
return status;
}
// tac 2009-09-15
//
IppStatus iden::BandPass_2D(Image2D &image_in, Image2D &image_bandpassed, const int feature_radius, const float hwhm_length)
{
/*//set status variable*/
IppStatus status;
Gaussian_Kernel GaussKernel(feature_radius, hwhm_length, image_in.get_width(), image_in.get_height());
Tophat_Kernel TopHatKernel(feature_radius, image_in.get_width(), image_in.get_height());
// int number_of_pixels = image_in.get_numberofpixels();
int step_size = image_in.get_stepsize();
// trim off extreme outliers (cut top .2% of data off
/*//Create and initialize intermediate images*/
Image2D image_gauss_col(image_in.get_height(), image_in.get_width());
Image2D image_gauss_rowcol(image_in.get_height(), image_in.get_width());
Image2D image_tophat(image_in.get_height(), image_in.get_width());
/*//Gaussian kernel convolution*/
status = ippiFilterColumn_32f_C1R(image_in.get_image2D() + GaussKernel.get_offset(),
step_size,
image_gauss_col.get_image2D() + GaussKernel.get_offset(),
step_size,
GaussKernel.get_ROI_size(),
GaussKernel.get_gaussian_kernel(),
GaussKernel.get_kernel_length(),
GaussKernel.get_anchor_point());
status = ippiFilterRow_32f_C1R(image_gauss_col.get_image2D() + GaussKernel.get_offset(),
step_size,
image_gauss_rowcol.get_image2D() + GaussKernel.get_offset(),
step_size,
GaussKernel.get_ROI_size(),
GaussKernel.get_gaussian_kernel(),
GaussKernel.get_kernel_length(),
GaussKernel.get_anchor_point());
/*//tophat kernel convolution/filterbox operation*/
status = ippiFilterBox_32f_C1R(image_in.get_image2D() + TopHatKernel.get_offset(), step_size,
image_tophat.get_image2D() + TopHatKernel.get_offset(), step_size,
TopHatKernel.get_ROI_size(), TopHatKernel.get_mask_size(),
TopHatKernel.get_anchor_point());
/*//subtract the two images*/
status = ippiSub_32f_C1R(image_tophat.get_image2D() + TopHatKernel.get_offset(), step_size,
image_gauss_rowcol.get_image2D()+TopHatKernel.get_offset(), step_size,
image_bandpassed.get_image2D() + TopHatKernel.get_offset(), step_size,
TopHatKernel.get_ROI_size());
/*//cutoff values below zero*/
status = ippiThreshold_LTVal_32f_C1IR(image_bandpassed.get_image2D() + TopHatKernel.get_offset(), step_size,
TopHatKernel.get_ROI_size(),0,0);
return status;
}
IppStatus BandPass_2D(Image2D &image_in, Image2D &image_bandpassed, const int feature_radius, const int hwhm_length)
{
//set status variable
IppStatus status;
Gaussian_Kernel GaussKernel(feature_radius, hwhm_length, image_in.get_width(), image_in.get_length());
Convolution_Kernel ConvolutionKernels(feature_radius, image_in.get_width(), image_in.get_length());
Tophat_Kernel TopHatKernel(feature_radius, image_in.get_width(), image_in.get_length());
int number_of_pixels = image_in.get_numberofpixels();
int step_size = image_in.get_stepsize();
//Create and initialize intermediate images
Image2D image_gauss_col(image_in.get_length(), image_in.get_width());
Image2D image_gauss_rowcol(image_in.get_length(), image_in.get_width());
Image2D image_tophat(image_in.get_length(), image_in.get_width());
//Gaussian kernel convolution
status = ippiFilterColumn_32f_C1R(image_in.get_image2D() + GaussKernel.get_offset(), step_size,
image_gauss_col.get_image2D() + GaussKernel.get_offset(), step_size,
GaussKernel.get_ROI_size(), GaussKernel.get_gaussian_kernel(),
GaussKernel.get_kernel_length(), GaussKernel.get_anchor_point());
status = ippiFilterRow_32f_C1R(image_gauss_col.get_image2D() + GaussKernel.get_offset(), step_size,
image_gauss_rowcol.get_image2D() + GaussKernel.get_offset(), step_size,
GaussKernel.get_ROI_size(), GaussKernel.get_gaussian_kernel(),
GaussKernel.get_kernel_length(), GaussKernel.get_anchor_point());
/*
//tophat kernel convolution/filterbox operation
status = ippiFilterBox_32f_C1R(image_in.get_image2D() + TopHatKernel.get_offset(), step_size,
image_tophat.get_image2D() + TopHatKernel.get_offset(), step_size,
TopHatKernel.get_ROI_size(), TopHatKernel.get_mask_size(),
TopHatKernel.get_anchor_point());
*/
//change by Eli Sloutskin: take away bias of square filtering kernel
status = ippiConvValid_32f_C1R(image_in.get_image2D(), step_size, image_in.get_ROIfull(),
ConvolutionKernels.get_circle_kernel(), ConvolutionKernels.get_kernel_step(), ConvolutionKernels.get_kernel_size(),
image_tophat.get_image2D() + ConvolutionKernels.get_offset(), step_size);
ippiDivC_32f_C1IR(3*feature_radius*feature_radius, image_tophat.get_image2D(),image_tophat.get_stepsize(),image_tophat.get_ROIfull());
//subtract the two images
status = ippiSub_32f_C1R(image_tophat.get_image2D() + TopHatKernel.get_offset(), step_size,
image_gauss_rowcol.get_image2D()+TopHatKernel.get_offset(), step_size,
image_bandpassed.get_image2D() + TopHatKernel.get_offset(), step_size,
TopHatKernel.get_ROI_size());
//cutoff values below zero
status = ippiThreshold_LTVal_32f_C1IR(image_bandpassed.get_image2D() + TopHatKernel.get_offset(), step_size,
TopHatKernel.get_ROI_size(),0,0);
return status;
}
Image2D<unsigned char> Image2DGrey::down_sample() const
{
Image2D newImage (get_width() / 2, get_height() / 2);
for (int y=0; y < newImage.get_height();y++)
{
int oldY = y * 2;
for (int x=0; x<newImage.get_width();x++)
{
int oldX = x * 2;
int sample1 = get_pixel(oldX, oldY);
int sample2 = get_pixel(oldX + 1, oldY);
int sample3 = get_pixel(oldX, oldY + 1);
int sample4 = get_pixel(oldX + 1, oldY + 1);
newImage.set_pixel(x,y, (sample1 + sample2 + sample3 + sample4) / 4);
}
}
return newImage;
}
IppStatus FindLocalMax_2D(Image2D &image_bpass, Image2D &image_bpass_thresh, Image2D &image_subtracted,
const int intensity_threshold, const int dilation_radius)
{
IppStatus status;
Image2D image_dilated(image_bpass.get_length(), image_bpass.get_width());
Dilation_Kernel DilationKernel(dilation_radius, image_bpass.get_width(), image_bpass.get_length());
//Threshold darker pixels in bandpassed image (in preparation for later subtraction)
RecenterImage(image_bpass);
status = ippiThreshold_LTVal_32f_C1R(image_bpass.get_image2D(), image_bpass.get_stepsize(),
image_bpass_thresh.get_image2D(), image_bpass_thresh.get_stepsize(),
image_bpass.get_ROIfull(), intensity_threshold, intensity_threshold);
//Dilate Bandpassed image with a circular kernel
status = ippiSet_32f_C1R(intensity_threshold, image_dilated.get_image2D(), image_dilated.get_stepsize(),
image_dilated.get_ROIfull());
status = ippiDilate_32f_C1R(
//image_bpass.get_image2D() + DilationKernel.get_offset(), image_bpass.get_stepsize(),
image_bpass_thresh.get_image2D() + DilationKernel.get_offset(), image_bpass_thresh.get_stepsize(),
image_dilated.get_image2D()+ DilationKernel.get_offset(), image_dilated.get_stepsize(),
DilationKernel.get_ROI_size(), DilationKernel.get_dilation_kernel(), DilationKernel.get_mask_size(),
DilationKernel.get_anchor_point());
//subtract, such that resulting array is negative to zero (for later exponentation)
status = ippiSub_32f_C1R(
image_dilated.get_image2D(), image_dilated.get_stepsize(),
image_bpass.get_image2D(), image_bpass.get_stepsize(),
image_subtracted.get_image2D(), image_subtracted.get_stepsize(),
image_bpass.get_ROIfull());
//exponentiate subtracted array, then threshold
status = ippiExp_32f_C1IR(image_subtracted.get_image2D(), image_subtracted.get_stepsize(),
image_subtracted.get_ROIfull());
status = ippiThreshold_LTValGTVal_32f_C1IR(image_subtracted.get_image2D(), image_subtracted.get_stepsize(),
image_subtracted.get_ROIfull(), 1-epsilon, 0, 1-epsilon, 1);
return status;
}
void Iden::process_frame(const Image2D & img_in,
unsigned int frame_number,
const Md_store * md_store_in,
Wrapper_i_plu & wrapper_out) const
{
Md_store * md_store_local = new Md_store();
if (! md_store_in)
md_store_local->add_elements(md_store_in);
float hwhm,thresh,top_cut,a,b;
int feature_rad,dilation_rad, mask_rad;
unsigned int avg_count;
// the parameters should be verified when, they are set, but the try
// can't hurt.
try
{
params_.get_value("threshold",thresh);
params_.get_value("p_rad",feature_rad);
params_.get_value("hwhm",hwhm);
params_.get_value("d_rad",dilation_rad);
params_.get_value("mask_rad",mask_rad);
params_.get_value("top_cut",top_cut);
}
catch(logic_error & e)
{
std::cerr<<"Iden::error parsing the parameters"<<std::endl;
std::cerr<<e.what()<<std::endl;
throw;
}
unsigned int height = img_in.get_height();
unsigned int width = img_in.get_width();
// object for holding band passed image
Image2D image_bpass(height,width);
// object for holding the thresholded band passed image
Image2D image_bpass_thresh(height,width);
// object that holds the local max
Image2D image_localmax(height,width);
// local mutable copy of image
Image2D image_in_local(img_in);
RecenterImage(image_in_local);
IppStatus status;
status = BandPass_2D(image_in_local,
image_bpass,
feature_rad,
hwhm);
status = FindLocalMax_2D(image_bpass,
image_bpass_thresh,
image_localmax,
thresh,
dilation_rad);
RecenterImage(image_bpass_thresh);
// get out massive nx9 array
int counter;
Ipp32f (*particledata)[9] =
ParticleStatistics(image_localmax,
image_bpass_thresh,
mask_rad,
feature_rad,
counter);
// set data in wrapper
wrapper_out.add_frame_data(particledata,frame_number,counter);
// set metadata in wrapper
// the wrapper takes responsibility for the object
wrapper_out.set_Md_store(frame_number,md_store_local);
// clean up wrapper
}
