void intersect(const Ty* X1, const Ty* X2, Ty* M, int d, int n1, int n2)
{
// compute the respective sums
Ty* hs1 = new Ty[n1];
Ty* hs2 = new Ty[n2];
column_sum(X1, d, n1, hs1);
column_sum(X2, d, n2, hs2);
// compute metrics
const Ty* v2 = X2;
for (int j = 0; j < n2; ++j, v2 += d)
{
const Ty* v1 = X1;
for (int i = 0; i < n1; ++i, v1 += d)
{
Ty s = 0;
for (int k = 0; k < d; ++k)
{
Ty u1 = v1[k];
Ty u2 = v2[k];
s += ((u1 < u2) ? u1 : u2);
}
Ty smax = ((hs1[i] > hs2[j]) ? hs1[i] : hs2[j]);
*M++ = ((smax > 0) ? s / smax : 1);
}
}
// release resources
delete[] hs1;
delete[] hs2;
}
void base_reg::base_score(const mematrix<double>& resid,
const int model,
const int interaction,
const int ngpreds,
const masked_matrix& invvarmatrix,
const int nullmodel) {
mematrix<double> oX = reg_data.extract_genotypes();
mematrix<double> X = apply_model(oX, model, interaction, ngpreds,
reg_data.is_interaction_excluded, false, nullmodel);
beta.reinit(X.ncol, 1);
sebeta.reinit(X.ncol, 1);
int length_beta = X.ncol;
double N = static_cast<double>(resid.nrow);
mematrix<double> tX = transpose(X);
if (invvarmatrix.length_of_mask != 0){
tX = tX * invvarmatrix.masked_data;
}
mematrix<double> u = tX * resid;
mematrix<double> v = tX * X;
mematrix<double> csum = column_sum(X);
csum = transpose(csum) * csum;
csum = csum * (1. / N);
v = v - csum;
// use cholesky to invert
LDLT <MatrixXd> Ch = LDLT < MatrixXd > (v.data.selfadjointView<Lower>());
// before was
// mematrix<double> v_i = invert(v);
beta.data = Ch.solve(v.data.adjoint() * u.data);
//TODO(maartenk): set size of v_i directly or remove mematrix class
mematrix<double> v_i = v;
v_i.data = Ch.solve(MatrixXd(length_beta, length_beta).
Identity(length_beta, length_beta));
double sr = 0.;
double srr = 0.;
for (int i = 0; i < resid.nrow; i++)
{
sr += resid[i];
srr += resid[i] * resid[i];
}
double mean_r = sr / N;
double sigma2_internal = (srr - N * mean_r * mean_r) / (N - beta.nrow);
for (int i = 0; i < beta.nrow; i++)
sebeta[i] = sqrt(v_i.get(i, i) * sigma2_internal);
mematrix<double> chi2 = transpose(u) * v_i * u;
chi2 = chi2 * (1. / sigma2_internal);
chi2_score = chi2[0];
}
void base_reg::base_score(mematrix<double>& resid, regdata& rdata, int verbose,
double tol_chol, int model, int interaction,
int ngpreds, const masked_matrix& invvarmatrix,
int nullmodel)
{
mematrix<double> oX = rdata.extract_genotypes();
mematrix<double> X = apply_model(oX, model, interaction, ngpreds,
rdata.is_interaction_excluded, false,
nullmodel);
beta.reinit(X.ncol, 1);
sebeta.reinit(X.ncol, 1);
double N = static_cast<double>(resid.nrow);
mematrix<double> tX = transpose(X);
if (invvarmatrix.length_of_mask != 0)
tX = tX * invvarmatrix.masked_data;
mematrix<double> u = tX * resid;
mematrix<double> v = tX * X;
mematrix<double> csum = column_sum(X);
csum = transpose(csum) * csum;
csum = csum * (1. / N);
v = v - csum;
// use cholesky to invert
mematrix<double> v_i = v;
cholesky2_mm(v_i, tol_chol);
chinv2_mm(v_i);
// before was
// mematrix<double> v_i = invert(v);
beta = v_i * u;
double sr = 0.;
double srr = 0.;
for (int i = 0; i < resid.nrow; i++)
{
sr += resid[i];
srr += resid[i] * resid[i];
}
double mean_r = sr / N;
double sigma2_internal = (srr - N * mean_r * mean_r) / (N - beta.nrow);
for (int i = 0; i < beta.nrow; i++)
sebeta[i] = sqrt(v_i.get(i, i) * sigma2_internal);
mematrix<double> chi2 = transpose(u) * v_i * u;
chi2 = chi2 * (1. / sigma2_internal);
chi2_score = chi2[0];
}
/* Calibration run. Aborting allowed at "safe" points where the scanner won't
* be left in a crap state. */
int sanei_canon_pp_calibrate(scanner_parameters *sp, char *cal_file)
{
int count, readnum, colournum, scanlinenum;
int outfile;
int scanline_size;
int scanline_count = 6;
/* Don't change this unless you also want to change do_adjust */
const int calibration_reads = 3;
unsigned char command_buffer[10];
image_segment image;
unsigned char *databuf;
char colours[3][6] = {"Red", "Green", "Blue"};
/* Calibration data is monochromatic (greyscale format) */
scanline_size = sp->scanheadwidth * 1.25;
/* 620P has to be difficult here... */
if (!(sp->type) ) scanline_count = 8;
/* Probably shouldn't have to abort *just* yet, but may as well check */
if (sp->abort_now) return -1;
DBG(40, "Calibrating %ix%i pixels calibration image "
"(%i bytes each scan).\n",
sp->scanheadwidth, scanline_count,
scanline_size * scanline_count);
/* Allocate memory for calibration data */
sp->blackweight = (unsigned long *)
calloc(sizeof(unsigned long), sp->scanheadwidth);
sp->redweight = (unsigned long *)
calloc(sizeof(unsigned long), sp->scanheadwidth);
sp->greenweight = (unsigned long *)
calloc(sizeof(unsigned long), sp->scanheadwidth);
sp->blueweight = (unsigned long *)
calloc(sizeof(unsigned long), sp->scanheadwidth);
/* The data buffer needs to hold a number of images (calibration_reads)
* per colour, each sp->scanheadwidth x scanline_count */
databuf = malloc(scanline_size * scanline_count * calibration_reads*3);
/* And allocate space for converted image data in this image_segment */
image.image_data = malloc(scanline_count * sp->scanheadwidth * 2 *
calibration_reads);
image.width = sp->scanheadwidth;
image.height = scanline_count * calibration_reads;
/* Sending the "dark calibration" command */
memcpy(command_buffer, cmd_calblack, 10);
/* Which includes the size of data we expect the scanner to return */
command_buffer[7] = ((scanline_size * scanline_count) & 0xff00) >> 8;
command_buffer[8] = (scanline_size * scanline_count) & 0xff;
DBG(40, "Step 1/3: Calibrating black level...\n");
for (readnum = 0; readnum < calibration_reads; readnum++)
{
DBG(40, " * Black scan number %d/%d.\n", readnum + 1,
calibration_reads);
if (sp->abort_now) return -1;
if (send_command(sp->port, command_buffer, 10, 100000, 5000000))
{
DBG(1, "Error reading black level!\n");
free (image.image_data);
free(databuf);
return -1;
}
/* Black reference data */
sanei_canon_pp_read(sp->port, scanline_size * scanline_count,
databuf +
(readnum * scanline_size * scanline_count));
}
/* Convert scanner format to a greyscale 16bpp image */
for (scanlinenum = 0;
scanlinenum < scanline_count * calibration_reads;
scanlinenum++)
{
convdata(databuf + (scanlinenum * scanline_size),
image.image_data +
(scanlinenum * sp->scanheadwidth*2),
sp->scanheadwidth, 1);
}
/* Take column totals */
for (count = 0; count < sp->scanheadwidth; count++)
{
/* Value is normalised as if we took 6 scanlines, even if we
* didn't (620P I'm looking at you!) */
sp->blackweight[count] = (column_sum(&image, count) * 6)
/ scanline_count >> 6;
}
/* 620P has to be difficult here... */
if (!(sp->type) )
{
scanline_count = 6;
image.height = scanline_count * calibration_reads;
}
DBG(40, "Step 2/3: Gamma tables...\n");
DBG(40, " * Requesting creation of new of gamma tables...\n");
if (sp->abort_now) return -1;
if (send_command(sp->port, cmd_cleargamma, 10, 100000, 5000000))
{
DBG(1,"Error sending gamma command!\n");
free (image.image_data);
free(databuf);
return -1;
}
DBG(20, " * Snoozing for 15 seconds while the scanner calibrates...");
usleep(15000000);
DBG(40, "done.\n");
DBG(40, " * Requesting gamma table values...");
if (send_command(sp->port, cmd_readgamma, 10, 100000, 10000000))
{
DBG(1,"Error sending gamma table request!\n");
free (image.image_data);
free(databuf);
return -1;
}
DBG(40, "done.\n");
DBG(40, " * Reading white-balance/gamma data... ");
sanei_canon_pp_read(sp->port, 32, sp->gamma);
DBG(40, "done.\n");
if (sp->abort_now) return -1;
memcpy(command_buffer, cmd_calcolour, 10);
/* Set up returned data size */
command_buffer[7] = ((scanline_size * scanline_count) & 0xff00) >> 8;
command_buffer[8] = (scanline_size * scanline_count) & 0xff;
DBG(40, "Step 3/3: Calibrating sensors...\n");
/* Now for the RGB high-points */
for (colournum = 1; colournum < 4; colournum++)
{
/* Set the colour we want to read */
command_buffer[3] = colournum;
for (readnum = 0; readnum < 3; readnum++)
{
DBG(10, " * %s sensors, scan number %d/%d.\n",
colours[colournum-1], readnum + 1,
calibration_reads);
if (sp->abort_now) return -1;
if (send_command(sp->port, command_buffer, 10,
100000, 5000000))
{
DBG(1,"Error sending scan request!");
free (image.image_data);
free(databuf);
return -1;
}
sanei_canon_pp_read(sp->port, scanline_size *
scanline_count, databuf +
(readnum * scanline_size *
scanline_count));
}
/* Convert colour data from scanner format to RGB data */
for (scanlinenum = 0; scanlinenum < scanline_count *
calibration_reads; scanlinenum++)
{
convdata(databuf + (scanlinenum * scanline_size),
image.image_data +
(scanlinenum * sp->scanheadwidth * 2),
sp->scanheadwidth, 1);
}
/* Sum each column of the image and store the results in sp */
for (count = 0; count < sp->scanheadwidth; count++)
{
if (colournum == 1)
sp->redweight[count] =
column_sum(&image, count) >> 6;
else if (colournum == 2)
sp->greenweight[count] =
column_sum(&image, count) >> 6;
else
sp->blueweight[count] =
column_sum(&image, count) >> 6;
}