void adjust_sigma(Simulator *sim, int steps, double step_size,
double factor)
{
double original_sigma = sim->sigma;
double best_sigma = sim->sigma;
double best_error = barcode_error(sim);
for (int step = -steps; step <= steps; step++) {
if (step == 0)
continue;
sim->sigma = original_sigma + step * step_size;
if (sim->sigma < 1.0)
continue;
compute_kernel(sim);
convolve_1d(sim->kernel_width, sim->kernel,
sim->width, sim->guess, sim->blur, 0, sim->width);
double error = barcode_error(sim);
// printf("sigma=%.2f error=%.2f\n", sim->sigma, error);
if (error < best_error) {
best_error = error;
best_sigma = sim->sigma;
}
}
sim->sigma = best_sigma * factor + original_sigma * (1.0 - factor);
compute_kernel(sim);
convolve_1d(sim->kernel_width, sim->kernel,
sim->width, sim->guess, sim->blur, 0, sim->width);
}
void check_and_compute() {
compute_kernel();
// calculate error
// not being done right now since we are doing a fixed no. of iterations
double *tmp;
tmp = temperature;
temperature = new_temperature;
new_temperature = tmp;
constrainBC();
if (iterations % CKP_FREQ == 0 || iterations > MAX_ITER) {
#ifdef CMK_MEM_CHECKPOINT
contribute(0, 0, CkReduction::concat, CkCallback(CkIndex_Main::report(), mainProxy));
#elif CMK_MESSAGE_LOGGING
if(iterations > MAX_ITER)
contribute(0, 0, CkReduction::concat, CkCallback(CkIndex_Main::report(), mainProxy));
else
AtSync();
#else
contribute(0, 0, CkReduction::concat, CkCallback(CkIndex_Main::report(), mainProxy));
#endif
} else {
doStep();
}
}
TEST(Kernel, Diagonal)
{
AbelianGroup X(0, 2);
X(0) = 1;
X(1) = 2;
AbelianGroup Y(0, 1);
Y(0) = 2;
MatrixQ f = {{5, 2}};
MatrixQList to_K;
MatrixQList from_K;
MatrixQList from_X;
MatrixQ id = {{1, 0}, {0, 1}};
from_X.emplace_back(id);
GroupWithMorphisms K =
compute_kernel(5, f, X, Y, MatrixQRefList(), ref(from_X));
EXPECT_EQ(0, K.group.free_rank());
ASSERT_EQ(1, K.group.tor_rank());
EXPECT_EQ(1, K.group(0));
}
static int compute_gainshift_kernel (Isis_Kernel_t *k, double *result, Isis_Hist_t *g, double *par, unsigned int num, /*{{{*/
int (*fun)(Isis_Hist_t *))
{
Isis_Rmf_t *rmf = k->rsp.rmf;
double *ylo=NULL, *yhi=NULL;
double *tmp, *shift_lo, *shift_hi;
double r0 = par[0]/KEV_ANGSTROM, slope = par[1];
unsigned int i, len, n;
int status = -1;
if (-1 == compute_kernel (k, result, g, par, num, fun))
return -1;
if ((par[0] < 0) || (par[1] == 0.0))
{
isis_vmesg(FAIL, I_ERROR, __FILE__, __LINE__,
"gainshift kernel: parameters (%g, %g) define an invalid grid",
par[0], par[1]);
return -1;
}
if (-1 == rmf->get_data_grid (rmf, &ylo, &yhi, &n, NULL))
return -1;
len = 3 * n * sizeof(double);
if (NULL == (tmp = (double *) ISIS_MALLOC (len)))
goto return_error;
shift_lo = tmp + n;
shift_hi = tmp + 2*n;
#define NEW_LAMBDA(y) (1.0/(1.0/y/slope - r0))
shift_lo[0] = NEW_LAMBDA(ylo[0]);
for (i = 1; i < n; i++)
{
shift_lo[i] = NEW_LAMBDA(ylo[i]);
shift_hi[i-1] = shift_lo[i];
}
shift_hi[n-1] = NEW_LAMBDA(yhi[n-1]);
if (-1 == rebin_histogram (result, ylo, yhi, n,
tmp, shift_lo, shift_hi, n))
{
ISIS_FREE(tmp);
isis_vmesg(FAIL, I_ERROR, __FILE__, __LINE__,
"gainshift kernel failed while rebinning histogram");
goto return_error;
}
memcpy ((char *)result, (char *)tmp, n * sizeof(double));
ISIS_FREE(tmp);
status = 0;
return_error:
ISIS_FREE(ylo);
ISIS_FREE(yhi);
return status;
}
GroupWithMorphisms compute_image(const std::size_t p, const MatrixQ& f,
const AbelianGroup& X, const AbelianGroup& Y)
{
MatrixQRefList to_X;
MatrixQList from_X = {MatrixQ::identity(f.width())};
GroupWithMorphisms K = compute_kernel(p, f, X, Y, to_X, ref(from_X));
MatrixQList to_X_2 = {MatrixQ::identity(f.width())};
MatrixQList from_X_2 = {f};
GroupWithMorphisms img =
compute_cokernel(p, f, Y, ref(to_X_2), ref(from_X_2));
return img;
}
GroupWithMorphisms compute_image(const mod_t p, const MatrixQ& f,
const AbelianGroup& X, const AbelianGroup& Y)
{
MatrixQRefList to_X_dummy;
MatrixQList from_X = {MatrixQ::identity(f.width())};
GroupWithMorphisms K = compute_kernel(p, f, X, Y, to_X_dummy, ref(from_X));
MatrixQList to_X_2 = {MatrixQ::identity(X.rank())};
MatrixQList from_X_2 = {f,MatrixQ::identity(X.rank())};//hacky, since id:X->X doesn't vanish on K.
//but due to the implementation, the columns of this will contain
//representatives in X for the generators of img.
GroupWithMorphisms img =
compute_cokernel(p, K.maps_from[0], X, ref(to_X_2), ref(from_X_2));
return img;
}
/** processes the actual fourier transformation
* does a fourier transformation. This part of the program is rather
* expensive to compute, so make sure you call this a minimum number of
* times.
*
* @param amp A handler for the LV2 plugin instance.
*/
void fftprocess(Amp * amp)
{
int i;
float *fourier_buffer = amp->fourier_buffer;
float output[FOURIER_SIZE];
bcopy(amp->fourier_buffer, amp->previous_buffer,
sizeof(float) * FOURIER_SIZE);
peek_buffer(fourier_buffer, amp->in_buffer, FOURIER_SIZE);
compute_kernel(amp);
#ifdef __OPENMP__
#pragma omp parallel for
#endif
for (i = 0; i < FOURIER_SIZE; i++) {
float inbuf[FOURIER_SIZE];
float kernel[FOURIER_SIZE];
//float* inbufp = (float*)inbuf; // pointer type
prefetch_buffer(inbuf, amp->in_buffer, FOURIER_SIZE, i);
#ifdef __SSE__
if (has_sse()){
average_kernels_sse(kernel, amp);
} else {
average_kernels(kernel, amp);
exit(EXIT_FAILURE);
}
#else
average_kernels(kernel, amp);
#endif
//bcopy(kernel, amp->fourier_buffer, sizeof(float) * FOURIER_SIZE);
output[i] = (amp->convolve_func) (inbuf, kernel);
assert( output[i] >= -1.0 && output[i] <= 1.0);
}
write_buffer(amp->out_buffer, output, FOURIER_SIZE);
read_buffer(NULL, amp->in_buffer, FOURIER_SIZE);
}
static int compute_yshift_kernel (Isis_Kernel_t *k, double *result, Isis_Hist_t *g, double *par, unsigned int num, /*{{{*/
int (*fun)(Isis_Hist_t *))
{
Isis_Rmf_t *rmf = k->rsp.rmf;
double *ylo=NULL, *yhi=NULL;
double dy = par[0];
unsigned int n;
int status = -1;
if (-1 == compute_kernel (k, result, g, par, num, fun))
return -1;
if (dy == 0.0)
return 0;
if (-1 == rmf->get_data_grid (rmf, &ylo, &yhi, &n, NULL))
return -1;
if (ylo[0] + dy > 0.0)
{
double *tmp, *shift_lo, *shift_hi;
unsigned int i, len;
len = 3 * n * sizeof(double);
if (NULL == (tmp = (double *) ISIS_MALLOC (len)))
goto return_error;
shift_lo = tmp + n;
shift_hi = tmp + 2*n;
/* dy > 0 moves features to longer wavelengths */
shift_lo[0] = ylo[0] - dy;
for (i = 1; i < n; i++)
{
shift_lo[i] = ylo[i] - dy;
shift_hi[i-1] = shift_lo[i];
}
shift_hi[n-1] = yhi[n-1] - dy;
if (-1 == rebin_histogram (result, ylo, yhi, n,
tmp, shift_lo, shift_hi, n))
{
ISIS_FREE(tmp);
isis_vmesg(FAIL, I_ERROR, __FILE__, __LINE__,
"shift kernel failed while rebinning histogram");
goto return_error;
}
memcpy ((char *)result, (char *)tmp, n * sizeof(double));
ISIS_FREE(tmp);
}
else
{
isis_vmesg(FAIL, I_ERROR, __FILE__, __LINE__, "offset=%g yields invalid grid", dy);
goto return_error;
}
status = 0;
return_error:
ISIS_FREE(ylo);
ISIS_FREE(yhi);
return status;
}
